semibin: semibin.xml annotate

annotate semibin.xml @ 3:8673617e7e09 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6

author	iuc
date	Tue, 28 Oct 2025 08:15:27 +0000
parents	9de6b5e570df
children

rev	line source
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	1 <tool id="semibin" name="SemiBin" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	2 <description>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	3 for Semi-supervised Metagenomic Binning
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	4 </description>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	5 <macros>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	6 <import>macros.xml</import>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	7 </macros>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	8 <expand macro="biotools"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	9 <expand macro="requirements"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	10 <expand macro="version"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	11 <command detect_errors="exit_code"><![CDATA[
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	12 #import re
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	13 #if $mode.select != "single":
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	14 #if $mode.align_select.align_select == "bam":
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	15 @BAM_FILES@
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	16 #else:
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	17 @STROBEALIGN_FILES@
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	18 #end if
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	19 #else:
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	20 @BAM_FILES@
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	21 #end if
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	22 @FASTA_FILES@
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	23 SemiBin2
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	24 #if $mode.select == 'single' or $mode.select == 'co'
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	25 single_easy_bin
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	26 #if $mode.select == 'single' and str($mode.environment) != ''
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	27 --environment '$mode.environment'
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	28 #end if
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	29 #if $mode.ref.select == "cached":
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	30 --reference-db-data-dir '$mode.ref.cached_db.fields.path'
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	31 #end if
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	32 #if $mode.ref.select == "taxonomy"
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	33 --taxonomy-annotation-table '$mode.ref.taxonomy_annotation_table'
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	34 #end if
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	35 #else
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	36 multi_easy_bin
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	37 --separator '$separator'
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	38 #if $mode.ref.select == "cached":
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	39 --reference-db-data-dir '$mode.ref.cached_db.fields.path'
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	40 #end if
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	41 #if $mode.ref.select == "taxonomy"
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	42 --taxonomy-annotation-table
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	43 #for $e in $mode.ref.taxonomy_annotation_table
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	44 '$e'
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	45 #end for
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	46 #end if
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	47 #end if
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	48 --input-fasta 'contigs.$input_fasta.ext'
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	49 #if $mode.select == "single":
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	50 --input-bam *.bam
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	51 #else:
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	52 #if $mode.align_select.align_select == "bam":
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	53 --input-bam *.bam
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	54 #else:
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	55 -a *.txt
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	56 #end if
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	57 #end if
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	58 --output 'output'
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	59 --cannot-name 'cannot'
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	60 @MIN_LEN@
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	61 --orf-finder '$orf_finder'
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	62 --random-seed $random_seed
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	63
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	64 #if $annot.ml_threshold:
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	65 --ml-threshold $annot.ml_threshold
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	66 #end if
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	67 --epoches $training.epoches
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	68 --batch-size $training.batch_size
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	69 --max-node $bin.max_node
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	70 --max-edges $bin.max_edges
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	71 --minfasta-kbs $bin.minfasta_kbs
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	72 #if ($mode.select == 'single' or $mode.select == 'co') and $extra_output and "pre_reclustering_bins" in $extra_output
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	73 --write-pre-reclustering-bins
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	74 #end if
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	75 --compression none
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	76 --threads \${GALAXY_SLOTS:-1}
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	77 --processes \${GALAXY_SLOTS:-1}
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	78 &&
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	79 echo "output" &&
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	80 ls output
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	81 ]]></command>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	82 <inputs>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	83 <conditional name="mode">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	84 <expand macro="mode_select"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	85 <when value="single">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	86 <expand macro="input-fasta-single"/>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	87 <expand macro="input-bam-single"/>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	88 <expand macro="ref-single"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	89 <expand macro="environment"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	90 </when>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	91 <when value="co">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	92 <expand macro="input-fasta-single"/>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	93 <conditional name="align_select">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	94 <expand macro="bam_or_strobealign"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	95 <when value="bam">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	96 <expand macro="input-bam-multi"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	97 </when>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	98 <when value="txt">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	99 <expand macro="input-txt"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	100 </when>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	101 </conditional>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	102 <expand macro="ref-single"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	103 </when>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	104 <when value="multi">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	105 <expand macro="input-fasta-multi"/>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	106 <conditional name="align_select">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	107 <expand macro="bam_or_strobealign"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	108 <when value="bam">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	109 <expand macro="input-bam-multi"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	110 </when>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	111 <when value="txt">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	112 <expand macro="input-txt"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	113 </when>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	114 </conditional>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	115 <expand macro="ref-multi"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	116 </when>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	117 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	118 <expand macro="min_len"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	119 <expand macro="orf-finder"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	120 <expand macro="random-seed"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	121 <section name="annot" title="Contig annotations" expanded="true">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	122 <expand macro="ml-threshold"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	123 </section>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	124 <section name="training" title="Training">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	125 <expand macro="epoches"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	126 <expand macro="batch-size"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	127 </section>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	128 <section name="bin" title="Binning">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	129 <expand macro="max-node"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	130 <expand macro="max-edges"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	131 <expand macro="minfasta-kbs"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	132 </section>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	133 <param name="extra_output" type="select" multiple="true" optional="true" label="Extra outputs" help="In addition to the training data">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	134 <option value="data">Training data</option>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	135 <option value="coverage">Coverage files</option>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	136 <option value="contigs">Contigs (if multiple sample)</option>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	137 <option value="pre_reclustering_bins">Pre-reclustering bins (only single sample and co-assembly)</option>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	138 </param>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	139 </inputs>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	140 <outputs>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	141 <collection name="output_pre_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering">
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	142 <filter>mode['select']!="multi" and extra_output and "pre_reclustering_bins" in extra_output</filter>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	143 <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/output_prerecluster_bins"/>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	144 </collection>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	145 <collection name="output_after_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins after reclustering">
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	146 <filter>mode['select']!="multi" and extra_output and "pre_reclustering_bins" in extra_output</filter>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	147 <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/output_recluster_bins"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	148 </collection>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	149 <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins">
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	150 <filter>mode['select']!="multi" and not "pre_reclustering_bins" in extra_output</filter>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	151 <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/output_bins"/>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	152 </collection>
1 2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	153 <collection name="multi_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering (multi_bins)">
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	154 <filter>mode['select']=="multi"</filter>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	155 <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/bins"/>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	156 </collection>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	157 <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data">
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	158 <filter>(mode['select']=="single" or mode['select']=="co") and extra_output and "data" in extra_output</filter>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	159 </data>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	160 <data name="single_data_split" format="csv" from_work_dir="output/data_split.csv" label="${tool.name} on ${on_string}: Split training data">
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	161 <filter>(mode['select']=="single" or mode['select']=="co") and extra_output and "data" in extra_output</filter>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	162 </data>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	163 <collection name="multi_data" type="list" label="${tool.name} on ${on_string}: Training data per sample">
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	164 <filter>mode['select']=="multi" and extra_output and "data" in extra_output</filter>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	165 <discover_datasets pattern="(?P<designation>.*)\/data.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	166 </collection>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	167 <collection name="multi_data_split" type="list" label="${tool.name} on ${on_string}: Split training data per sample">
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	168 <filter>mode['select']=="multi" and extra_output and "data" in extra_output</filter>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	169 <discover_datasets pattern="(?P<designation>.*)\/data_split.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	170 </collection>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	171 <expand macro="generate_sequence_features_extra_outputs_main"/>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	172 </outputs>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	173 <tests>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	174 <test expect_num_outputs="5">
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	175 <conditional name="mode">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	176 <param name="select" value="single"/>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	177 <param name="input_fasta" ftype="fasta.gz" value="input_single.fasta.gz"/>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	178 <param name="input_bam" ftype="bam" value="input_single.bam"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	179 <conditional name="ref">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	180 <param name="select" value="taxonomy"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	181 <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	182 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	183 <param name="environment" value="human_gut"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	184 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	185 <conditional name="min_len">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	186 <param name="method" value="min-len"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	187 <param name="min_len" value="0" />
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	188 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	189 <param name="orf_finder" value="prodigal"/>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	190 <param name="random_seed" value="0"/>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	191 <section name="training">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	192 <param name="epoches" value="20"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	193 <param name="batch_size" value="2048"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	194 </section>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	195 <section name="bin">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	196 <param name="max_node" value="1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	197 <param name="max_edges" value="200"/>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	198 <param name="minfasta_kbs" value="200"/>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	199 </section>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	200 <param name="extra_output" value="data,coverage,contigs"/>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	201 <output name="single_data" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	202 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	203 <has_text text="g1k_0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	204 <has_text text="g4k_7"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	205 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	206 </output>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	207 <output name="single_data_split" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	208 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	209 <has_text text="g1k_0_1"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	210 <has_text text="g1k_6_2"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	211 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	212 </output>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	213 <output name="single_cov" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	214 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	215 <has_text text="g1k_0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	216 <has_text text="0.027"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	217 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	218 </output>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	219 <output name="single_split_cov" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	220 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	221 <has_size value="1" delta="1"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	222 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	223 </output>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	224 </test>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	225 <test expect_num_outputs="5">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	226 <conditional name="mode">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	227 <param name="select" value="single"/>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	228 <param name="input_fasta" ftype="fasta.bz2" value="input_single.fasta.bz2"/>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	229 <param name="input_bam" ftype="bam" value="input_single.bam"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	230 <conditional name="ref">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	231 <param name="select" value="ml"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	232 </conditional>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	233 <param name="environment" value="human_gut"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	234 </conditional>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	235 <conditional name="min_len">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	236 <param name="method" value="min-len"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	237 <param name="min_len" value="0" />
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	238 </conditional>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	239 <param name="orf_finder" value="prodigal"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	240 <param name="random_seed" value="0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	241 <section name="training">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	242 <param name="epoches" value="20"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	243 <param name="batch_size" value="2048"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	244 </section>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	245 <section name="bin">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	246 <param name="max_node" value="1"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	247 <param name="max_edges" value="200"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	248 <param name="minfasta_kbs" value="200"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	249 </section>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	250 <param name="extra_output" value="data,coverage,contigs"/>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	251 <output name="single_data" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	252 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	253 <has_text text="g1k_0"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	254 <has_text text="g4k_7"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	255 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	256 </output>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	257 <output name="single_data_split" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	258 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	259 <has_text text="g1k_0_1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	260 <has_text text="g1k_6_2"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	261 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	262 </output>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	263 <output name="single_cov" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	264 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	265 <has_text text="g1k_0"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	266 <has_text text="0.027"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	267 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	268 </output>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	269 <output name="single_split_cov" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	270 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	271 <has_size value="1" delta="1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	272 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	273 </output>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	274 </test>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	275 <test expect_num_outputs="3">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	276 <conditional name="mode">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	277 <param name="select" value="co"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	278 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	279 <conditional name="align_select">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	280 <param name="align_select" value="bam"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	281 <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	282 </conditional>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	283 <conditional name="ref">
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	284 <param name="select" value="ml"/>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	285 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	286 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	287 <conditional name="min_len">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	288 <param name="method" value="ratio"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	289 <param name="ratio" value="0.05"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	290 </conditional>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	291 <param name="orf_finder" value="fast-naive"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	292 <param name="random_seed" value="0"/>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	293 <section name="training">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	294 <param name="epoches" value="20"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	295 <param name="batch_size" value="2048"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	296 </section>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	297 <section name="bin">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	298 <param name="max_node" value="1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	299 <param name="max_edges" value="200"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	300 <param name="minfasta_kbs" value="200"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	301 </section>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	302 <param name="extra_output" value="coverage"/>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	303 <output_collection name="co_cov_bam" count="5">
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	304 <element name="0" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	305 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	306 <has_text text="g1k_0"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	307 <has_text text="g2k_7"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	308 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	309 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	310 <element name="1" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	311 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	312 <has_text text="g1k_0"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	313 <has_text text="g2k_7"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	314 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	315 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	316 <element name="4" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	317 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	318 <has_text text="g1k_0"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	319 <has_text text="g2k_7"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	320 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	321 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	322 </output_collection>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	323 <output_collection name="co_split_cov_bam" count="5">
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	324 <element name="0" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	325 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	326 <has_text text="g1k_0_1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	327 <has_text text="g2k_7_2"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	328 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	329 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	330 <element name="1" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	331 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	332 <has_text text="g1k_0_1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	333 <has_text text="g2k_7_2"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	334 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	335 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	336 <element name="2" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	337 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	338 <has_text text="g1k_0_1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	339 <has_text text="g2k_7_2"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	340 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	341 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	342 </output_collection>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	343 </test>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	344 <test expect_num_outputs="3">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	345 <conditional name="mode">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	346 <param name="select" value="co"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	347 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	348 <conditional name="align_select">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	349 <param name="align_select" value="bam"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	350 <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	351 </conditional>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	352 <conditional name="ref">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	353 <param name="select" value="taxonomy"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	354 <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	355 </conditional>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	356 </conditional>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	357 <conditional name="min_len">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	358 <param name="method" value="ratio"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	359 <param name="ratio" value="0.05"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	360 </conditional>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	361 <param name="orf_finder" value="fast-naive"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	362 <param name="random_seed" value="0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	363 <section name="training">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	364 <param name="epoches" value="20"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	365 <param name="batch_size" value="2048"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	366 </section>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	367 <section name="bin">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	368 <param name="max_node" value="1"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	369 <param name="max_edges" value="200"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	370 <param name="minfasta_kbs" value="200"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	371 </section>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	372 <param name="extra_output" value="coverage"/>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	373 <output_collection name="co_cov_bam" count="5">
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	374 <element name="0" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	375 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	376 <has_text text="g1k_0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	377 <has_text text="g2k_7"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	378 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	379 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	380 <element name="1" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	381 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	382 <has_text text="g1k_0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	383 <has_text text="g2k_7"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	384 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	385 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	386 <element name="4" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	387 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	388 <has_text text="g1k_0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	389 <has_text text="g2k_7"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	390 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	391 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	392 </output_collection>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	393 <output_collection name="co_split_cov_bam" count="5">
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	394 <element name="0" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	395 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	396 <has_text text="g1k_0_1"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	397 <has_text text="g2k_7_2"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	398 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	399 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	400 <element name="1" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	401 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	402 <has_text text="g1k_0_1"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	403 <has_text text="g2k_7_2"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	404 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	405 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	406 <element name="2" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	407 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	408 <has_text text="g1k_0_1"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	409 <has_text text="g2k_7_2"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	410 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	411 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	412 </output_collection>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	413 </test>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	414 <test expect_num_outputs="3">
1 2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	415 <conditional name="mode">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	416 <param name="select" value="co"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	417 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	418 <conditional name="align_select">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	419 <param name="align_select" value="bam"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	420 <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	421 </conditional>
1 2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	422 <conditional name="ref">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	423 <param name="select" value="taxonomy"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	424 <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	425 </conditional>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	426 </conditional>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	427 <conditional name="min_len">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	428 <param name="method" value="ratio"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	429 <param name="ratio" value="0.05"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	430 </conditional>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	431 <param name="orf_finder" value="fast-naive"/>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	432 <param name="random_seed" value="0"/>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	433 <section name="annot">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	434 <param name="ml_threshold" value="0"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	435 </section>
1 2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	436 <section name="training">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	437 <param name="epoches" value="20"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	438 <param name="batch_size" value="2048"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	439 </section>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	440 <section name="bin">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	441 <param name="max_node" value="1"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	442 <param name="max_edges" value="200"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	443 <param name="minfasta_kbs" value="200"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	444 </section>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	445 <param name="extra_output" value="coverage"/>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	446 <output_collection name="co_cov_bam" count="5">
1 2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	447 <element name="0" ftype="csv">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	448 <assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	449 <has_text text="g1k_0"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	450 <has_text text="g2k_7"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	451 </assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	452 </element>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	453 <element name="1" ftype="csv">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	454 <assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	455 <has_text text="g1k_0"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	456 <has_text text="g2k_7"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	457 </assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	458 </element>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	459 <element name="4" ftype="csv">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	460 <assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	461 <has_text text="g1k_0"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	462 <has_text text="g2k_7"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	463 </assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	464 </element>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	465 </output_collection>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	466 <output_collection name="co_split_cov_bam" count="5">
1 2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	467 <element name="0" ftype="csv">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	468 <assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	469 <has_text text="g1k_0_1"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	470 <has_text text="g2k_7_2"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	471 </assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	472 </element>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	473 <element name="1" ftype="csv">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	474 <assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	475 <has_text text="g1k_0_1"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	476 <has_text text="g2k_7_2"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	477 </assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	478 </element>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	479 <element name="2" ftype="csv">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	480 <assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	481 <has_text text="g1k_0_1"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	482 <has_text text="g2k_7_2"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	483 </assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	484 </element>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	485 </output_collection>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	486 </test>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	487 <test expect_num_outputs="1">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	488 <conditional name="mode">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	489 <param name="select" value="single"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	490 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	491 <param name="input_bam" ftype="bam" value="input_single.bam"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	492 <conditional name="ref">
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	493 <param name="select" value="cached"/>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	494 <param name="cached_db" value="test-db"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	495 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	496 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	497 <conditional name="min_len">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	498 <param name="method" value="ratio"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	499 <param name="ratio" value="0.05"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	500 </conditional>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	501 <param name="orf_finder" value="fast-naive"/>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	502 <param name="random_seed" value="0"/>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	503 <section name="annot">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	504 <param name="ml_threshold" value="0"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	505 </section>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	506 <section name="training">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	507 <param name="epoches" value="20"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	508 <param name="batch_size" value="2048"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	509 </section>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	510 <section name="bin">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	511 <param name="max_node" value="1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	512 <param name="max_edges" value="200"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	513 <param name="minfasta_kbs" value="200"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	514 </section>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	515 </test>
1 2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	516 <test expect_num_outputs="2">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	517 <conditional name="mode">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	518 <param name="select" value="single"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	519 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	520 <param name="input_bam" ftype="bam" value="input_single.bam"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	521 <conditional name="ref">
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	522 <param name="select" value="cached"/>
1 2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	523 <param name="cached_db" value="test-db"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	524 </conditional>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	525 </conditional>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	526 <conditional name="min_len">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	527 <param name="method" value="ratio"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	528 <param name="ratio" value="0.05"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	529 </conditional>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	530 <param name="orf_finder" value="fast-naive"/>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	531 <param name="random_seed" value="0"/>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	532 <section name="annot">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	533 <param name="ml_threshold" value="0"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	534 </section>
1 2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	535 <section name="training">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	536 <param name="epoches" value="20"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	537 <param name="batch_size" value="2048"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	538 </section>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	539 <section name="bin">
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	540 <param name="max_node" value="1"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	541 <param name="max_edges" value="200"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	542 <param name="minfasta_kbs" value="200"/>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	543 </section>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	544 <param name="extra_output" value="pre_reclustering_bins"/>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	545 <output_collection name="output_pre_recluster_bins">
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	546 <element name="SemiBin_0" ftype="fasta">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	547 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	548 <has_text text="g1k_0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	549 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	550 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	551 <element name="SemiBin_1" ftype="fasta">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	552 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	553 <has_text text="g2k_0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	554 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	555 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	556 <element name="SemiBin_2" ftype="fasta">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	557 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	558 <has_text text="g3k_0"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	559 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	560 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	561 </output_collection>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	562 <output_collection name="output_after_recluster_bins" count="1">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	563 <element name="SemiBin_30" ftype="fasta">
1 2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	564 <assert_contents>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	565 <has_text text="g3k_0"/>
1 2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	566 </assert_contents>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	567 </element>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	568 </output_collection>
2eeff5d4a5de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d iuc parents: 0 diff changeset	569 </test>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	570 <test expect_num_outputs="8">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	571 <conditional name="mode">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	572 <param name="select" value="multi"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	573 <conditional name="multi_fasta">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	574 <param name="select" value="concatenated"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	575 <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	576 </conditional>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	577 <conditional name="align_select">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	578 <param name="align_select" value="bam"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	579 <param name="input_bam" ftype="bam" value="input_multi_sorted1.bam,input_multi_sorted2.bam,input_multi_sorted3.bam,input_multi_sorted4.bam,input_multi_sorted5.bam,input_multi_sorted6.bam,input_multi_sorted7.bam,input_multi_sorted8.bam,input_multi_sorted9.bam,input_multi_sorted10.bam"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	580 </conditional>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	581 <conditional name="ref">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	582 <param name="select" value="taxonomy"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	583 <param name="taxonomy_annotation_table" value="taxonomy.tsv,taxonomy_2.tsv,taxonomy_3.tsv,taxonomy_4.tsv,taxonomy_5.tsv,taxonomy_6.tsv,taxonomy_7.tsv,taxonomy_8.tsv,taxonomy_9.tsv,taxonomy_10.tsv"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	584 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	585 </conditional>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	586 <conditional name="min_len">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	587 <param name="method" value="ratio"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	588 <param name="ratio" value="0.05"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	589 </conditional>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	590 <param name="orf_finder" value="fast-naive"/>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	591 <param name="random_seed" value="0"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	592 <section name="training">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	593 <param name="epoches" value="20"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	594 <param name="batch_size" value="2048"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	595 </section>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	596 <section name="bin">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	597 <param name="max_node" value="1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	598 <param name="max_edges" value="200"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	599 <param name="minfasta_kbs" value="200"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	600 </section>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	601 <param name="extra_output" value="data,coverage,contigs"/>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	602 <output_collection name="multi_bins" count="0"/>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	603 <output_collection name="multi_data" count="10">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	604 <element name="S8" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	605 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	606 <has_text text="g1k_0,"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	607 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	608 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	609 </output_collection>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	610 <output_collection name="multi_data_split" count="10">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	611 <element name="S8" ftype="csv">
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	612 <assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	613 <has_text text="g1k_0_1,"/>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	614 </assert_contents>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	615 </element>
9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	616 </output_collection>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	617 <output_collection name="multi_cov_bam" count="10">
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	618 <element name="8" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	619 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	620 <has_text text="S1:g1k_5,"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	621 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	622 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	623 </output_collection>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	624 <output_collection name="multi_cov_sample_bam" count="10">
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	625 <element name="S8" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	626 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	627 <has_text text="g1k_3"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	628 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	629 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	630 </output_collection>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	631 <output_collection name="multi_split_cov_bam" count="10">
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	632 <element name="8" ftype="csv">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	633 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	634 <has_text text="S1:g1k_5_1,0."/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	635 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	636 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	637 </output_collection>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	638 <output_collection name="multi_split_cov_sample_bam" count="10">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	639 <element name="8" ftype="csv">
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	640 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	641 <has_text text="g1k_3_1"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	642 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	643 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	644 </output_collection>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	645 <output_collection name="multi_contigs" count="10">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	646 <element name="S8" ftype="fasta">
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	647 <assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	648 <has_text text=">g1k_0"/>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	649 </assert_contents>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	650 </element>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	651 </output_collection>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	652 </test>
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	653 <test expect_num_outputs="6">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	654 <conditional name="mode">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	655 <param name="select" value="co"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	656 <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	657 <conditional name="align_select">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	658 <param name="align_select" value="txt"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	659 <param name="abundance" ftype="txt" value="strobealign_1.txt,strobealign_2.txt,strobealign_3.txt,strobealign_4.txt,strobealign_5.txt"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	660 </conditional>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	661 <conditional name="ref">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	662 <param name="select" value="taxonomy"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	663 <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	664 </conditional>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	665 </conditional>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	666 <conditional name="min_len">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	667 <param name="method" value="ratio"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	668 <param name="ratio" value="0.05"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	669 </conditional>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	670 <param name="orf_finder" value="fast-naive"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	671 <param name="random_seed" value="0"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	672 <section name="annot">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	673 <param name="ml_threshold" value="0"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	674 </section>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	675 <section name="training">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	676 <param name="epoches" value="20"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	677 <param name="batch_size" value="2048"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	678 </section>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	679 <section name="bin">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	680 <param name="max_node" value="0.15"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	681 <param name="max_edges" value="20"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	682 <param name="minfasta_kbs" value="20"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	683 </section>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	684 <param name="extra_output" value="data,coverage,contigs,pre_reclustering_bins"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	685 </test>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	686 <test expect_num_outputs="6">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	687 <conditional name="mode">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	688 <param name="select" value="multi"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	689 <conditional name="multi_fasta">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	690 <param name="select" value="concatenated"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	691 <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	692 </conditional>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	693 <conditional name="align_select">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	694 <param name="align_select" value="txt"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	695 <param name="abundance" ftype="txt" value="strobealign_1.txt,strobealign_2.txt,strobealign_3.txt,strobealign_4.txt,strobealign_5.txt"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	696 </conditional>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	697 <conditional name="ref">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	698 <param name="select" value="taxonomy"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	699 <param name="taxonomy_annotation_table" value="taxonomy.tsv,taxonomy_2.tsv,taxonomy_3.tsv,taxonomy_4.tsv,taxonomy_5.tsv,taxonomy_6.tsv,taxonomy_7.tsv,taxonomy_8.tsv,taxonomy_9.tsv,taxonomy_10.tsv"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	700 </conditional>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	701 </conditional>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	702 <conditional name="min_len">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	703 <param name="method" value="ratio"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	704 <param name="ratio" value="0.05"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	705 </conditional>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	706 <param name="orf_finder" value="fast-naive"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	707 <param name="random_seed" value="0"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	708 <section name="annot">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	709 <param name="ml_threshold" value="0"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	710 </section>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	711 <section name="training">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	712 <param name="epoches" value="20"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	713 <param name="batch_size" value="2048"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	714 </section>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	715 <section name="bin">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	716 <param name="max_node" value="0.15"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	717 <param name="max_edges" value="30"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	718 <param name="minfasta_kbs" value="30"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	719 </section>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	720 <param name="extra_output" value="data,coverage,contigs"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	721 <output_collection name="multi_bins" count="10"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	722 <output_collection name="multi_data" count="10">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	723 <element name="S8" ftype="csv">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	724 <assert_contents>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	725 <has_text text="g1k_0,"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	726 </assert_contents>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	727 </element>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	728 </output_collection>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	729 <output_collection name="multi_data_split" count="10">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	730 <element name="S8" ftype="csv">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	731 <assert_contents>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	732 <has_text text="g1k_0_1,"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	733 </assert_contents>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	734 </element>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	735 </output_collection>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	736 <output_collection name="multi_cov_txt" count="10">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	737 <element name="S8" ftype="csv">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	738 <assert_contents>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	739 <has_text text="g1k_5,"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	740 </assert_contents>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	741 </element>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	742 </output_collection>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	743 <output_collection name="multi_split_cov_txt" count="10">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	744 <element name="S8" ftype="csv">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	745 <assert_contents>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	746 <has_text text="g1k_5_1,1."/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	747 </assert_contents>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	748 </element>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	749 </output_collection>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	750 <output_collection name="multi_contigs" count="10">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	751 <element name="S8" ftype="fasta">
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	752 <assert_contents>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	753 <has_text text=">g1k_0"/>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	754 </assert_contents>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	755 </element>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	756 </output_collection>
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	757 </test>
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	758 </tests>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	759 <help><![CDATA[
3 8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	760 Please note that there is a known issue with Semibin2 where results may be inconsistent across runs on different, despite a set seed. This may cause issues with reproducibility.
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	761 For more information, see this [issue]{https://github.com/BigDataBiology/SemiBin/issues/186} on their repository: https://github.com/BigDataBiology/SemiBin/issues/186
8673617e7e09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6 iuc parents: 2 diff changeset	762
0 d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	763 @HELP_HEADER@
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	764
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	765 Inputs
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	766 ======
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	767
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	768 @HELP_INPUT_FASTA@
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	769 @HELP_INPUT_BAM@
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	770
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	771 ]]></help>
d1f0be443b8b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4 iuc parents: diff changeset	772 <expand macro="citations"/>
2 9de6b5e570df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b iuc parents: 1 diff changeset	773 </tool>

Mercurial > repos > iuc > semibin

annotate semibin.xml @ 3:8673617e7e09 draft default tip