test_upload: samtools_stats.xml annotate

annotate samtools_stats.xml @ 0:12bc610792b2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty

author	mvdbeek
date	Tue, 25 Sep 2018 04:09:34 -0400
parents
children

rev	line source
0 12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	1 <tool id="samtools_stats" name="Stats" version="2.0.1">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	2 <description>generate statistics for BAM dataset</description>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	3 <macros>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	4 <import>macros.xml</import>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	5 </macros>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	6 <expand macro="requirements"/>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	7 <expand macro="stdio"/>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	8 <expand macro="version_command"/>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	9 <command><![CDATA[
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	10 #if $use_reference.use_ref_selector == "yes":
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	11 #if $use_reference.reference_source.reference_source_selector == "history":
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	12 ln -s '${use_reference.reference_source.ref_file}' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	13 samtools faidx `basename '${use_reference.reference_source.ref_file}'` &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	14 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	15 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	16
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	17 samtools stats
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	18 '${input_file}'
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	19 --coverage ${coverage_min},${coverage_max},${coverage_step}
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	20 ${remove_dups}
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	21
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	22 #if str( $filter_by_flags.filter_flags ) == "filter":
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	23 #if $filter_by_flags.require_flags:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	24 --required-flag ${sum([int(flag) for flag in str($filter_by_flags.require_flags).split(',')])}
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	25 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	26 #if $filter_by_flags.exclude_flags:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	27 --filtering-flag ${sum([int(flag) for flag in str($filter_by_flags.exclude_flags).split(',')])}
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	28 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	29 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	30
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	31 --GC-depth ${gc_depth}
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	32 --insert-size ${insert_size}
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	33
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	34 ## The code below is commented out because using -I/--id options causes the following exception
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	35 ## Samtools-htslib: init_group_id() header parsing not yet implemented
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	36 ##if str($read_group) != "":
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	37 ## -I "${read_group}"
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	38 ##end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	39
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	40 #if str($read_length):
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	41 --read-length ${read_length}
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	42 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	43
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	44 --most-inserts ${most_inserts}
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	45 --trim-quality ${trim_quality}
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	46
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	47 #if $use_reference.use_ref_selector == "yes":
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	48 #if $use_reference.reference_source.reference_source_selector != "history":
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	49 --ref-seq '${use_reference.reference_source.ref_file.fields.path}'
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	50 #else:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	51 --ref-seq '${use_reference.reference_source.ref_file}'
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	52 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	53 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	54 > '${output}'
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	55
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	56 #if $split_output.split_output_selector == "yes":
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	57 #set outputs_to_split = str($split_output.generate_tables).split(',')
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	58 && mkdir split &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	59 echo ${split_output.generate_tables}
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	60
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	61 #if 'sn' in $outputs_to_split:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	62 && echo "# Summary Numbers" > 'split/Summary numbers.tab' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	63 echo "" >> 'split/Summary numbers.tab' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	64 if grep -q ^SN '${output}'; then
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	65 grep ^SN '${output}' \| cut -f 2- >> 'split/Summary numbers.tab';
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	66 fi
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	67 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	68
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	69 #if 'ffq' in $outputs_to_split:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	70 && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > 'split/First Fragment Qualities.tab' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	71 if grep -q ^FFQ '${output}'; then
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	72 grep ^FFQ '${output}' \| cut -f 2- >> 'split/First Fragment Qualities.tab';
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	73 fi
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	74 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	75
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	76 #if 'lfq' in $outputs_to_split:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	77 && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > 'split/Last Fragment Qualities.tab' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	78 if grep -q ^LFQ '${output}'; then
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	79 grep ^LFQ '${output}' \| cut -f 2- >> 'split/Last Fragment Qualities.tab';
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	80 fi
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	81 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	82
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	83 #if 'mpc' in $outputs_to_split:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	84 && echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > 'split/Mismatches per cycle.tab' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	85 if grep -q ^MPC '${output}'; then
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	86 grep ^MPC '${output}' \| cut -f 2- >> 'split/Mismatches per cycle.tab';
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	87 fi
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	88 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	89
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	90 #if 'gcf' in $outputs_to_split:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	91 && echo "# GC Content of first fragments" > 'split/GC Content of first fragments.tab' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	92 if grep -q ^GCF '${output}'; then
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	93 grep ^GCF '${output}' \| cut -f 2- >> 'split/GC Content of first fragments.tab';
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	94 fi
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	95 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	96
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	97 #if 'gcl' in $outputs_to_split:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	98 && echo "# GC Content of last fragments" > 'split/GC Content of last fragments.tab' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	99 if grep -q ^GCL '${output}'; then
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	100 grep ^GCL '${output}' \| cut -f 2- >> 'split/GC Content of last fragments.tab';
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	101 fi
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	102 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	103
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	104 #if 'gcc' in $outputs_to_split:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	105 && echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > 'split/ACGT content per cycle.tab' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	106 if grep -q ^GCC '${output}'; then
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	107 grep ^GCC '${output}' \| cut -f 2- >> 'split/ACGT content per cycle.tab';
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	108 fi
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	109 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	110
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	111 #if 'is' in $outputs_to_split:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	112 && echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > 'split/Insert sizes.tab' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	113 if grep -q ^IS '${output}'; then
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	114 grep ^IS '${output}' \| cut -f 2- >> 'split/Insert sizes.tab';
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	115 fi
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	116 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	117
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	118 #if 'rl' in $outputs_to_split:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	119 && echo "# Read lengths. The columns are: read length, count" > 'split/Read lengths.tab' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	120 if grep -q ^RL '${output}'; then
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	121 grep ^RL '${output}' \| cut -f 2- >> 'split/Read lengths.tab';
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	122 fi
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	123 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	124
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	125 #if 'id' in $outputs_to_split:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	126 && echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > 'split/Indel distribution.tab' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	127 if grep -q ^ID '${output}'; then
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	128 grep ^ID '${output}' \| cut -f 2- >> 'split/Indel distribution.tab';
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	129 fi
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	130 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	131
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	132 #if 'ic' in $outputs_to_split:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	133 && echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" > 'split/Indels per cycle.tab' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	134 if grep -q ^IC '${output}'; then
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	135 grep ^IC '${output}' \| cut -f 2- >> 'split/Indels per cycle.tab';
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	136 fi
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	137 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	138
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	139 #if 'cov' in $outputs_to_split:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	140 && echo "# Coverage distribution" > 'split/Coverage distribution.tab' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	141 if grep -q ^COV '${output}'; then
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	142 grep ^COV '${output}' \| cut -f 2- >> 'split/Coverage distribution.tab';
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	143 fi
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	144 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	145
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	146 #if 'gcd' in $outputs_to_split:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	147 && echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > 'split/GC depth.tab' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	148 if grep -q ^GCD '${output}'; then
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	149 grep ^GCD '${output}' \| cut -f 2- >> 'split/GC depth.tab';
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	150 fi
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	151 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	152 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	153 ]]></command>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	154 <inputs>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	155 <param name="input_file" type="data" format="sam,bam" label="BAM file" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	156 <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="Minimum coverage" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	157 <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="Maximum coverage" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	158 <param name="coverage_step" type="integer" value="1" label="Coverage step" help="Step value for coverage" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	159 <param name="remove_dups" argument="--remove-dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False"
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	160 label="Exclude reads marked as duplicates" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	161 <conditional name="split_output">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	162 <param name="split_output_selector" type="select" label="Output" help="Select between one single output or separate outputs for each statistics">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	163 <option value="no" selected="True">One single summary file</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	164 <option value="yes">Separate datasets for each statistic</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	165 </param>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	166 <when value="no" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	167 <when value="yes">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	168 <param name="generate_tables" type="select" display="checkboxes" multiple="True" label="Desired output files">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	169 <option value="sn">Summary numbers</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	170 <option value="ffq">First Fragment Qualities</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	171 <option value="lfq">Last Fragment Qualities</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	172 <option value="mpc">Mismatches per cycle</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	173 <option value="gcf">GC Content of first fragments</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	174 <option value="gcl">GC Content of last fragments</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	175 <option value="gcc">ACGT content per cycle</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	176 <option value="is">Insert sizes</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	177 <option value="rl">Read lengths</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	178 <option value="id">Indel distribution</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	179 <option value="ic">Indels per cycle</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	180 <option value="cov">Coverage distribution</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	181 <option value="gcd">GC depth</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	182 </param>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	183 </when>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	184 </conditional>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	185 <conditional name="filter_by_flags">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	186 <param name="filter_flags" type="select" label="Filter by SAM flags" help="More info on the flags: https://samtools.github.io/hts-specs/SAMv1.pdf">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	187 <option value="nofilter" selected="True">Do not filter</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	188 <option value="filter">Filter by flags to exclude or require</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	189 </param>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	190 <when value="filter">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	191 <param name="require_flags" argument="-f" type="select" display="checkboxes" multiple="True" label="Require">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	192 <option value="1">Read is paired</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	193 <option value="2">Read is mapped in a proper pair</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	194 <option value="4">The read is unmapped</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	195 <option value="8">The mate is unmapped</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	196 <option value="16">Read strand</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	197 <option value="32">Mate strand</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	198 <option value="64">Read is the first in a pair</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	199 <option value="128">Read is the second in a pair</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	200 <option value="256">The alignment or this read is not primary</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	201 <option value="512">The read fails platform/vendor quality checks</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	202 <option value="1024">The read is a PCR or optical duplicate</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	203 </param>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	204 <param name="exclude_flags" argument="-F" type="select" display="checkboxes" multiple="True" label="Exclude">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	205 <option value="1">Read is paired</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	206 <option value="2">Read is mapped in a proper pair</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	207 <option value="4">The read is unmapped</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	208 <option value="8">The mate is unmapped</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	209 <option value="16">Read strand</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	210 <option value="32">Mate strand</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	211 <option value="64">Read is the first in a pair</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	212 <option value="128">Read is the second in a pair</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	213 <option value="256">The alignment or this read is not primary</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	214 <option value="512">The read fails platform/vendor quality checks</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	215 <option value="1024">The read is a PCR or optical duplicate</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	216 </param>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	217 </when>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	218 <when value="nofilter" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	219
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	220 </conditional>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	221 <param name="gc_depth" argument="--GC-depth" type="float" value="20000" label="Size of GC-depth bins" help="Decreasing bin size increases memory requirement" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	222 <param name="insert_size" argument="--insert-size" type="integer" value="8000" label="Maximum insert size" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	223 <!--
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	224
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	225 The -I option of samtools stats returns the following message in version 1.2:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	226
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	227 Samtools-htslib: init_group_id() header parsing not yet implemented
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	228 Abort trap: 6
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	229
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	230 Because of this the section below is commented out until this stats bug is fixed
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	231
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	232 <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" >
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	233 <options>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	234 <filter type="data_meta" ref="input_file" key="read_groups" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	235 </options>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	236 </param>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	237
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	238 -->
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	239
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	240 <param name="read_length" argument="--read-length" type="integer" value="" optional="true" label="Minimum read length to generate statistics for" help="No cutoff if left empty"/>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	241 <param name="most_inserts" argument="--most-inserts" type="float" value="0.99" label="Report only the main part of inserts" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	242 <param name="trim_quality" argument="--trim-quality" type="integer" value="0" label="BWA trim parameter" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	243
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	244 <conditional name="use_reference">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	245 <param name="use_ref_selector" argument="--ref-seq" type="select" label="Use reference sequence" help="Required for GC-depth and mismatches-per-cycle calculation">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	246 <option value="yes">Use reference</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	247 <option selected="True" value="no">Do not use reference</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	248 </param>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	249 <when value="yes">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	250 <conditional name="reference_source">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	251 <param name="reference_source_selector" type="select" label="Choose a reference sequence for GC depth">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	252 <option value="cached">Locally cached</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	253 <option value="history">History</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	254 </param>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	255 <when value="cached">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	256 <param name="ref_file" type="select" label="Using genome">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	257 <options from_data_table="fasta_indexes">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	258 <filter type="data_meta" ref="input_file" key="dbkey" column="1" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	259 </options>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	260 </param>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	261 </when>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	262 <when value="history">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	263 <param name="ref_file" type="data" format="fasta" label="Using file" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	264 </when>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	265 </conditional>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	266 </when>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	267 <when value="no" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	268 </conditional>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	269
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	270 </inputs>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	271
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	272 <outputs>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	273 <data name="output" format="tabular" label="${tool.name} on ${on_string}">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	274 <discover_datasets pattern="(?P<designation>.+)\.tab" ext="tabular" visible="true" directory="split" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	275 </data>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	276 </outputs>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	277 <tests>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	278 <test>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	279 <param name="input_file" value="samtools_stats_input.bam" ftype="bam" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	280 <param name="use_ref_selector" value="yes" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	281 <param name="reference_source_selector" value="history" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	282 <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	283 <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	284 </test>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	285 <test>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	286 <param name="input_file" value="samtools_stats_input.bam" ftype="bam" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	287 <param name="use_ref_selector" value="yes" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	288 <param name="reference_source_selector" value="history" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	289 <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	290 <param name="split_output_selector" value="yes" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	291 <param name="generate_tables" value="sn,mpc,gcc" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	292 <output name="output" file="samtools_stats_out2.tab" lines_diff="4">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	293 <discovered_dataset designation="Summary numbers" ftype="tabular" file="samtools_stats_out2__sn.tab" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	294 <discovered_dataset designation="ACGT content per cycle" ftype="tabular" file="samtools_stats_out2__gcc.tab" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	295 <discovered_dataset designation="Mismatches per cycle" ftype="tabular" file="samtools_stats_out2__mpc.tab" />
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	296 </output>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	297 </test>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	298 </tests>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	299 <help><![CDATA[
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	300 What it does
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	301
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	302 This tool runs the ``samtools stats`` command.
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	303 ]]></help>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	304 <expand macro="citations"/>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	305 </tool>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty mvdbeek parents: diff changeset	306

Mercurial > repos > mvdbeek > test_upload

annotate samtools_stats.xml @ 0:12bc610792b2 draft default tip