hybpiper: hybpiper.xml annotate

annotate hybpiper.xml @ 0:91a16438e849 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8

author	iuc
date	Sat, 23 Sep 2023 16:49:12 +0000
parents
children

rev	line source
0 91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	1 <tool id="hybpiper" name="HybPiper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	2 <description>Analyse targeted sequence capture data</description>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	3 <macros>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	4 <import>macros.xml</import>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	5 </macros>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	6 <expand macro="xrefs"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	7 <expand macro="requirements"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	8 <command detect_errors="exit_code"><![CDATA[
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	9
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	10 ## sample name checking
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	11 #import re
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	12 #def check_sample_name($sample_name):
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	13 #if re.search(r'[^A-Za-z0-9_\-]', $sample_name):
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	14 printf '%s\n'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	15 'ERROR: special characters detected in sample identifier.'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	16 'Identifiers may only contain letters, numbers, underscores and hyphens.'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	17 'Check the identifier for the following sample:'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	18 '${sample_name}'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	19 1>&2
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	20 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	21 exit 1
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	22 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	23 #end if
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	24 #end def
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	25
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	26 ## set up files
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	27 ln -s '${targetfile_dna}' ./target_file.fasta
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	28 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	29
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	30 ###############################
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	31 ## hybpiper check_targetfile ##
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	32 ###############################
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	33
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	34 #if str( $job_conditional.hybpiper_job ) == "check_and_fix_targetfile":
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	35 hybpiper check_targetfile
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	36 --targetfile_dna target_file.fasta
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	37 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	38
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	39 mv fix_targetfile*.ctl hybpiper.ctl
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	40 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	41
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	42 hybpiper fix_targetfile
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	43 --targetfile_dna target_file.fasta
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	44 --allow_gene_removal
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	45 hybpiper.ctl
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	46 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	47
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	48 #######################
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	49 ## hybpiper assemble ##
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	50 #######################
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	51
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	52 #elif str( $job_conditional.hybpiper_job ) == "assemble":
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	53 #set sample_prefix = str($job_conditional.paired_input.element_identifier)
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	54
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	55 $check_sample_name($sample_prefix)
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	56
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	57 hybpiper assemble
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	58 --readfiles
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	59 '${job_conditional.paired_input.forward}'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	60 '${job_conditional.paired_input.reverse}'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	61 --targetfile_dna target_file.fasta
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	62 --diamond
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	63 --cpu \${GALAXY_SLOTS:-1}
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	64 --prefix '${sample_prefix}'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	65 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	66
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	67 tar -cvf '${hybpiper_archive}' --directory='${sample_prefix}' .
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	68 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	69
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	70 #######################################
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	71 ## hybpiper stats/retrieve_sequences ##
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	72 #######################################
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	73
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	74 #elif str( $job_conditional.hybpiper_job ) == "stats":
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	75
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	76 ## check logic of requested items
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	77 #unless $job_conditional.stats_type_select or $job_conditional.sequence_type_select:
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	78 printf '%s\n'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	79 'ERROR: No outputs selected.'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	80 1>&2
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	81 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	82 exit 1
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	83 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	84 #end unless
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	85 #if $job_conditional.heatmap and not $job_conditional.stats_type_select:
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	86 printf '%s\n'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	87 'ERROR: heatmap requested, but no stats selected.'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	88 1>&2
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	89 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	90 exit 1
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	91 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	92 #end if
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	93
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	94 #for $sample in $job_conditional.hybpiper_results
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	95 #set sample_prefix = str($sample.element_identifier)
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	96
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	97 $check_sample_name($sample_prefix)
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	98
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	99 mkdir -p '${sample_prefix}'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	100 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	101
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	102 tar -xf '${sample}' -C '${sample_prefix}'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	103 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	104
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	105 echo '${sample_prefix}' >> namelist.txt
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	106 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	107 #end for
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	108
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	109 ## Produce a stats file for each requested output type
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	110 #for $stats_output in $job_conditional.stats_type_select:
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	111 hybpiper stats
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	112 --targetfile_dna target_file.fasta
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	113 --stats_filename 'stats.${stats_output}'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	114 --seq_lengths_filename 'seq_lengths.${stats_output}'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	115 '${stats_output}'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	116 namelist.txt
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	117 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	118
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	119 ## Produce heatmaps if selected
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	120 #if $job_conditional.heatmap:
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	121 hybpiper recovery_heatmap
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	122 --heatmap_filename 'heatmap.${stats_output}'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	123 --heatmap_filetype svg
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	124 'seq_lengths.${stats_output}.tsv'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	125 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	126 #end if
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	127 #end for
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	128
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	129 ## Produce sequences for each requested type
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	130 #for $sequence_output in $job_conditional.sequence_type_select:
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	131 mkdir 'fasta.${sequence_output}'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	132 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	133 hybpiper retrieve_sequences
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	134 --targetfile_dna target_file.fasta
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	135 --sample_names namelist.txt
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	136 --fasta_dir 'fasta.${sequence_output}'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	137 '${sequence_output}'
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	138 &&
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	139 #end for
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	140 #end if
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	141
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	142 wait
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	143
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	144 ]]></command>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	145
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	146 <inputs>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	147 <param argument="--targetfile_dna" type="data" format="fasta" label="Target file" help="Target file in FASTA format" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	148
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	149 <conditional name="job_conditional">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	150 <param name="hybpiper_job" type="select" label="Type of hybpiper run">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	151 <option value="check_and_fix_targetfile">Check and fix targetfile</option>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	152 <option value="assemble" selected="true">Assemble target loci</option>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	153 <option value="stats">Extract sequences and/or stats from Hybpiper runs</option>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	154 </param>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	155
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	156 <when value="check_and_fix_targetfile"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	157
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	158 <when value="assemble">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	159 <param name="paired_input" format="fastqsanger" type="data_collection" collection_type="paired" label="Input reads" help="Your reads must be in a paired collection. See below for more information." />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	160 </when>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	161
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	162 <when value="stats">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	163 <param name="hybpiper_results" type="data_collection" collection_type="list" format="tar" multiple="true" label="Results from Hybpiper assemble runs" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	164 <param name="stats_type_select" type="select" label="Choose statistics to report" display="checkboxes" multiple="true" optional="true">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	165 <option value="gene" selected="true">Gene</option>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	166 <option value="supercontig">Supercontig</option>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	167 </param>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	168 <param name="heatmap" type="boolean" checked="false" label="Produce a heatmap for each of the selected statistics" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	169 <param name="sequence_type_select" type="select" display="checkboxes" label="Choose sequences to extract" multiple="true" optional="true">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	170 <option value="dna" selected="true">DNA</option>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	171 <option value="aa">Amino acid</option>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	172 <option value="intron">Intron</option>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	173 <option value="supercontig">Supercontig</option>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	174 </param>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	175 </when>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	176 </conditional>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	177 </inputs>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	178
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	179 <outputs>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	180 <!-- check_targetfile output -->
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	181 <data name="fixed_targetfile" label="${targetfile_dna.element_identifier} (fixed)" format="fasta" from_work_dir="target_file_fixed.fasta">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	182 <filter>job_conditional['hybpiper_job'] == 'check_and_fix_targetfile'</filter>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	183 </data>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	184 <collection type="list" name="output_targetfile" label="Hybpiper logs for ${targetfile_dna.element_identifier}">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	185 <data name="targetfile_ctl_file" label="Hybpiper .ctl file for ${on_string}" format="txt" from_work_dir="hybpiper.ctl" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	186 <data name="targetfile_report" label="Hybpiper targetfile report" format="tabular" from_work_dir="fix_targetfile_report.tsv" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	187 <filter>job_conditional['hybpiper_job'] == 'check_and_fix_targetfile'</filter>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	188 </collection>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	189
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	190 <!-- assemble output -->
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	191 <data name="hybpiper_archive" format="tar">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	192 <filter>job_conditional['hybpiper_job'] == 'assemble'</filter>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	193 </data>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	194
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	195 <!-- stats / stats output -->
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	196 <collection name="hybpiper_stats" type="list" label="Hybpiper statistics">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	197 <data name="stats_gene" label="Hybpiper statistics (gene)" format="tabular" from_work_dir="stats.gene.tsv">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	198 <actions>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	199 <action name="column_names" type="metadata" default="Name,NumReads,ReadsMapped,PctOnTarget,GenesMapped,GenesWithContigs,GenesWithSeqs,GenesAt25pct,GenesAt50pct,GenesAt75pct,GenesAt150pct,ParalogWarningsLong,ParalogWarningsDepth,GenesWithoutStitchedContigs,GenesWithStitchedContigs,GenesWithStitchedContigsSkipped,GenesWithChimeraWarning,TotalBasesRecovered" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	200 </actions>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	201 </data>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	202 <data name="stats_supercontig" label="Hybpiper statistics (supercontig)" format="tabular" from_work_dir="stats.supercontig.tsv">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	203 <actions>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	204 <action name="column_names" type="metadata" default="Name,NumReads,ReadsMapped,PctOnTarget,GenesMapped,GenesWithContigs,GenesWithSeqs,GenesAt25pct,GenesAt50pct,GenesAt75pct,GenesAt150pct,ParalogWarningsLong,ParalogWarningsDepth,GenesWithoutStitchedContigs,GenesWithStitchedContigs,GenesWithStitchedContigsSkipped,GenesWithChimeraWarning,TotalBasesRecovered" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	205 </actions>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	206 </data>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	207 <data name="seqlengths_gene" label="Assembled sequence lengths (gene)" format="tabular" from_work_dir="seq_lengths.gene.tsv"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	208 <data name="seqlengths_supercontig" label="Assembled sequence lengths (supercontig)" format="tabular" from_work_dir="seq_lengths.supercontig.tsv">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	209 </data>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	210 <filter>job_conditional['hybpiper_job'] == 'stats' and ('gene' in job_conditional['stats_type_select'] or 'supercontig' in job_conditional['stats_type_select'])</filter>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	211 </collection>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	212
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	213 <!-- stats/heatmap output -->
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	214 <collection name="hybpiper_heatmaps" type="list" label="Hybpiper heatmaps">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	215 <discover_datasets pattern="heatmap\.(?P<designation>.+)\.svg" format="svg" recurse="false" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	216 <filter>job_conditional['hybpiper_job'] == 'stats' and job_conditional['heatmap'] and job_conditional['heatmap'] is true</filter>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	217 </collection>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	218
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	219 <!-- stats/sequences output -->
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	220 <collection name="dna_sequences" type="list" label="DNA sequences">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	221 <discover_datasets pattern="(?P<designation>.+)\.FNA" format="fasta" directory="fasta.dna" recurse="false" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	222 <filter>job_conditional['hybpiper_job'] == 'stats' and 'dna' in job_conditional['sequence_type_select']</filter>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	223 </collection>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	224 <collection name="aa_sequences" type="list" label="Amino acid sequences">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	225 <discover_datasets pattern="(?P<designation>.+)\.FAA" format="fasta" directory="fasta.aa" recurse="false" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	226 <filter>job_conditional['hybpiper_job'] == 'stats' and 'aa' in job_conditional['sequence_type_select']</filter>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	227 </collection>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	228 <collection name="intron_sequences" type="list" label="Intron sequences">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	229 <discover_datasets pattern="(?P<designation>.+)\.fasta" format="fasta" directory="fasta.intron" recurse="false" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	230 <filter>job_conditional['hybpiper_job'] == 'stats' and 'intron' in job_conditional['sequence_type_select']</filter>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	231 </collection>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	232 <collection name="supercontig_sequences" type="list" label="Supercontig sequences">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	233 <discover_datasets pattern="(?P<designation>.+)\.fasta" format="fasta" directory="fasta.supercontig" recurse="false" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	234 <filter>job_conditional['hybpiper_job'] == 'stats' and 'supercontig' in job_conditional['sequence_type_select']</filter>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	235 </collection>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	236
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	237 <!-- dummy output, in case the user deselects everything -->
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	238 <data name="dummy_output" label="Stats or sequences from Hybpiper runs" from_work_dir="namelist.txt" format="txt">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	239 <filter>job_conditional['hybpiper_job'] == 'stats' and not (job_conditional['stats_type_select'] or job_conditional['sequence_type_select']) </filter>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	240 </data>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	241
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	242 </outputs>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	243 <tests>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	244
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	245 <!-- test1: check and fix targetfile -->
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	246 <test expect_num_outputs="4">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	247 <param name="targetfile_dna" value="test_targets.fasta.gz"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	248 <conditional name="job_conditional">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	249 <param name="hybpiper_job" value="check_and_fix_targetfile"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	250 </conditional>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	251 <output name="fixed_targetfile" file="test1_out.fasta"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	252 <output_collection name="output_targetfile" type="list" count="2">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	253 <element name="targetfile_ctl_file" file="test1_out.ctl"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	254 <element name="targetfile_report" file="test1_out.tsv"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	255 </output_collection>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	256 </test>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	257
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	258 <!-- test2: assemble with paired collection -->
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	259 <!-- Not possible to test stats unless element_identifier can be set. -->
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	260 <test expect_failure="true">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	261 <param name="targetfile_dna" value="test_targets.fasta.gz"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	262 <conditional name="job_conditional">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	263 <param name="hybpiper_job" value="assemble"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	264 <param name="paired_input">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	265 <collection type="paired">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	266 <element name="forward" ftype="fastqsanger.gz" value="NZ874_R1_test.fastq.gz" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	267 <element name="reverse" ftype="fastqsanger.gz" value="NZ874_R2_test.fastq.gz" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	268 </collection>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	269 </param>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	270 </conditional>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	271 <!-- <output name="hybpiper_archive">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	272 <assert_contents>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	273 <has_size value="2386944" delta="200000" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	274 </assert_contents>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	275 </output> -->
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	276 </test>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	277
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	278 <!-- test3: all stats output -->
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	279 <test expect_num_outputs="10">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	280 <param name="targetfile_dna" value="test_targets.fasta.gz"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	281 <conditional name="job_conditional">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	282 <param name="hybpiper_job" value="stats"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	283 <param name="hybpiper_results" >
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	284 <collection type="list">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	285 <element name="NZ874" value="NZ874.tar.gz" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	286 </collection>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	287 </param>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	288 <param name="stats_type_select" value="gene,supercontig"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	289 <param name="heatmap" value="true"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	290 <param name="sequence_type_select" value="dna,aa,intron,supercontig"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	291 </conditional>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	292 <output_collection name="hybpiper_stats" type="list" count="4" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	293 <output_collection name="hybpiper_heatmaps" type="list" count="2">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	294 </output_collection>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	295 <output_collection name="dna_sequences" type="list" count="13">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	296 </output_collection>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	297 <output_collection name="aa_sequences" type="list" count="13">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	298 </output_collection>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	299 <output_collection name="intron_sequences" type="list" count="13">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	300 </output_collection>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	301 <output_collection name="supercontig_sequences" type="list" count="13">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	302 </output_collection>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	303 </test>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	304
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	305 <!-- test4: no output selected -->
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	306 <test expect_failure="true">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	307 <param name="targetfile_dna" value="test_targets.fasta.gz"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	308 <conditional name="job_conditional">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	309 <param name="hybpiper_job" value="stats"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	310 <param name="hybpiper_results" >
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	311 <collection type="list">
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	312 <element name="NZ874" value="NZ874.tar.gz" />
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	313 </collection>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	314 </param>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	315 <param name="stats_type_select" value=""/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	316 <param name="heatmap" value="true"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	317 <param name="sequence_type_select" value=""/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	318 </conditional>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	319 </test>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	320
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	321 </tests>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	322 <help><![CDATA[
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	323
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	324 Using HybPiper on Galaxy
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	325 ------------------------
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	326
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	327 Input
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	328 ~~~~~
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	329
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	330 On Galaxy, you have to use paired collections as input for
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	331 HybPiper assemblies. HybPiper relies on the directory hierarchy it creates for each
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	332 sample during assembly. The hierarchy is based on the name of the
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	333 sample, which you provide to Galaxy as the identifier in the collection.
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	334
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	335 Using paired collections
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	336 ~~~~~~~~~~~~~~~~~~~~~~~~
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	337
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	338 If you have your sequencing reads in individual datasets, you can easily organise them into a paired
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	339 collection. See the Galaxy training material on `using dataset
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	340 collections <https://gxy.io/GTN:T00146>`__
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	341 for a step-by-step guide.
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	342
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	343 Note: because HybPiper uses sample
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	344 identifiers to create directories, you can't use special characters
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	345 in your sample identifiers. The only allowed characters are letters,
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	346 numbers, underscores and hyphens.
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	347
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	348 You can't use single-end and unpaired reads as input to Hybpiper on Galaxy.
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	349
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	350 Running HybPiper
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	351 ~~~~~~~~~~~~~~~~
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	352
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	353 The following HybPiper analyses are available on Galaxy:
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	354
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	355 1. Check your target file and fix issues (optional)
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	356 2. Assemble target loci per-sample
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	357 3. Extract sequences and summary statistics
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	358
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	359 Use the Type of hybpiper run drop-down to select an analysis.
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	360
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	361 .. class:: infomark
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	362
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	363 What it does
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	364 ------------
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	365
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	366 HybPiper was designed for processing targeted sequence capture data. In
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	367 targeted sequence capture, DNA sequencing libraries are enriched for
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	368 gene regions of interest. This is used for sequencing many loci
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	369 simultaneously based on bait sequences.
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	370
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	371 HybPiper is a suite of scripts that wrap and connect other tools to
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	372 extract target sequences from the sequencing reads. The HybPiper
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	373 pipeline starts with high-throughput sequencing reads (for example from
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	374 Illumina MiSeq), and assigns them to target genes using DIAMOND. The
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	375 reads are distributed to separate directories, where they are assembled
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	376 separately using SPAdes. The main output is a collection of FASTA files
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	377 of the (in frame) CDS portion of the sample for each target region. You
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	378 can also generate a separate collections of files with the translated
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	379 protein sequences, the intronic regions flanking each exon, and putative
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	380 paralog sequences.
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	381
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	382 For more information, please see `the HybPiper
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	383 wiki <https://github.com/mossmatters/HybPiper/wiki>`__.
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	384
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	385
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	386 ]]></help>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	387 <expand macro="citations"/>
91a16438e849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper commit b439a8bebdd20955135572a15672a12a166d7ff8 iuc parents: diff changeset	388 </tool>

Mercurial > repos > iuc > hybpiper

annotate hybpiper.xml @ 0:91a16438e849 draft default tip