samtools_stats: samtools_stats.xml annotate

annotate samtools_stats.xml @ 2:b02596e3d7a3 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_stats commit de7140295cce07e1bc1697e51dab4271c8d7a8a6

author	devteam
date	Fri, 18 Dec 2015 19:47:08 -0500
parents	cc56fc603e53
children	45c568e7f1f9

rev	line source
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	1 <tool id="samtools_stats" name="Stats" version="2.0">
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	2 <description>generate statistics for BAM dataset</description>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	3 <macros>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	4 <import>macros.xml</import>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	5 </macros>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	6 <expand macro="requirements"></expand>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	7 <expand macro="stdio"></expand>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	8 <expand macro="version_command"></expand>
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	9 <command><![CDATA[
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	10 #if $use_reference.use_ref_selector == "yes":
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	11 #if $use_reference.reference_source.reference_source_selector == "history":
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	12 ln -s "${use_reference.reference_source.ref_file}" && samtools faidx `basename "${use_reference.reference_source.ref_file}"` && samtools stats
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	13 #else:
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	14 samtools stats
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	15 #end if
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	16 #else:
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	17 samtools stats
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	18 #end if
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	19 "${input_file}"
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	20 --coverage ${coverage_min},${coverage_max},${coverage_step}
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	21 ${remove_dups}
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	22 #if str( $filter_by_flags.filter_flags ) == "filter":
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	23 #if $filter_by_flags.require_flags:
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	24 --required-flag ${sum([int(flag) for flag in str($filter_by_flags.require_flags).split(',')])}
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	25 #end if
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	26 #if $filter_by_flags.exclude_flags:
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	27 --filtering-flag ${sum([int(flag) for flag in str($filter_by_flags.exclude_flags).split(',')])}
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	28 #end if
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	29 #end if
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	30 --GC-depth ${gc_depth}
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	31 --insert-size ${insert_size}
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	32
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	33 ## The code below is commented out because using -I/--id options causes the following exception
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	34 ## Samtools-htslib: init_group_id() header parsing not yet implemented
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	35
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	36 ##if str($read_group) != "":
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	37 ## -I "${read_group}"
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	38 ##end if
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	39
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	40 #if str($read_length) != "0":
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	41 --read-length "${read_length}"
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	42 #end if
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	43 --most-inserts ${most_inserts}
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	44 --trim-quality ${trim_quality}
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	45 #if $use_reference.use_ref_selector == "yes":
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	46 #if $use_reference.reference_source.reference_source_selector != "history":
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	47 --ref-seq "${use_reference.reference_source.ref_file.fields.path}"
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	48 #else:
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	49 --ref-seq "${use_reference.reference_source.ref_file}"
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	50 #end if
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	51 #end if
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	52 > "${output}"
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	53 #if $split_output.split_output_selector == "yes":
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	54 #set outputs_to_split = str($split_output.generate_tables).split(',')
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	55 && mkdir split && echo ${split_output.generate_tables} &&
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	56
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	57 #if 'sn' in $outputs_to_split:
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	58 echo "# Summary Numbers\n" > "split/Summary numbers.tab" &&
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	59 grep -q ^SN "${output}" ; if [ $? = 0 ] ; then grep ^SN "${output}" \| cut -f 2- >> "split/Summary numbers.tab" ; fi &&
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	60 #end if
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	61
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	62 #if 'ffq' in $outputs_to_split:
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	63 echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > "split/First Fragment Qualities.tab" &&
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	64 grep -q ^FFQ "${output}" ; if [ $? = 0 ] ; then grep ^FFQ "${output}" \| cut -f 2- >> "split/First Fragment Qualities.tab" ; fi &&
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	65 #end if
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	66
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	67 #if 'lfq' in $outputs_to_split:
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	68 echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > "split/Last Fragment Qualities.tab" &&
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	69 grep -q ^LFQ "${output}" ; if [ $? = 0 ] ; then grep ^LFQ "${output}" \| cut -f 2- >> "split/Last Fragment Qualities.tab" ; fi &&
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	70 #end if
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	71
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	72 #if 'mpc' in $outputs_to_split:
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	73 echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > "split/Mismatches per cycle.tab" &&
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	74 grep -q ^MPC "${output}" ; if [ $? = 0 ] ; then grep ^MPC "${output}" \| cut -f 2- >> "split/Mismatches per cycle.tab" ; fi &&
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	75 #end if
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	76
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	77 #if 'gcf' in $outputs_to_split:
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	78 echo "# GC Content of first fragments" > "split/GC Content of first fragments.tab" &&
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	79 grep -q ^GCF "${output}" ; if [ $? = 0 ] ; then grep ^GCF "${output}" \| cut -f 2- >> "split/GC Content of first fragments.tab" ; fi &&
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	80 #end if
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	81
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	82 #if 'gcl' in $outputs_to_split:
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	83 echo "# GC Content of last fragments" > "split/GC Content of last fragments.tab" &&
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	84 grep -q ^GCL "${output}" ; if [ $? = 0 ] ; then grep ^GCL "${output}" \| cut -f 2- >> "split/GC Content of last fragments.tab" ; fi &&
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	85 #end if
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	86
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	87 #if 'gcc' in $outputs_to_split:
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	88 echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > "split/ACGT content per cycle.tab" &&
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	89 grep -q ^GCC "${output}" ; if [ $? = 0 ] ; then grep ^GCC "${output}" \| cut -f 2- >> "split/ACGT content per cycle.tab" ; fi &&
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	90 #end if
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	91
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	92 #if 'is' in $outputs_to_split:
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	93 echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > "split/Insert sizes.tab" &&
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	94 grep -q ^IS "${output}" ; if [ $? = 0 ] ; then grep ^IS "${output}" \| cut -f 2- >> "split/Insert sizes.tab" ; fi &&
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	95 #end if
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	96
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	97 #if 'rl' in $outputs_to_split:
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	98 echo "# Read lengths. The columns are: read length, count" > "split/Read lengths.tab" &&
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	99 grep -q ^RL "${output}" ; if [ $? = 0 ] ; then grep ^RL "${output}" \| cut -f 2- >> "split/Read lengths.tab" ; fi &&
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	100 #end if
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	101
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	102 #if 'id' in $outputs_to_split:
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	103 echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > "split/Indel distribution.tab" &&
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	104 grep -q ^ID "${output}" ; if [ $? = 0 ] ; then grep ^ID "${output}" \| cut -f 2- >> "split/Indel distribution.tab" ; fi &&
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	105 #end if
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	106
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	107 #if 'ic' in $outputs_to_split:
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	108 echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" > "split/Indels per cycle.tab" &&
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	109 grep -q ^IC "${output}" ; if [ $? = 0 ] ; then grep ^IC "${output}" \| cut -f 2- >> "split/Indels per cycle.tab" ; fi &&
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	110 #end if
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	111
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	112 #if 'cov' in $outputs_to_split:
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	113 echo "# Coverage distribution" > "split/Coverage distribution.tab" &&
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	114 grep -q ^COV "${output}" ; if [ $? = 0 ] ; then grep ^COV "${output}" \| cut -f 2- >> "split/Coverage distribution.tab" ; fi &&
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	115 #end if
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	116
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	117 #if 'gcd' in $outputs_to_split:
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	118 echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > "split/GC depth.tab" &&
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	119 grep -q ^GCD "${output}" ; if [ $? = 0 ] ; then grep ^GCD "${output}" \| cut -f 2- >> "split/GC depth.tab" ; fi &&
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	120 #end if
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	121
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	122 ## Unix true command below
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	123
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	124 true
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	125
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	126 #end if
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	127 ]]></command>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	128 <inputs>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	129 <param name="input_file" type="data" format="sam,bam" label="BAM file" />
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	130 <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="minimum coverage value for --coverage option"/>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	131 <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="maximum coverage value for --coverage option"/>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	132 <param name="coverage_step" type="integer" value="1" label="Coverage step" help="step value for --coverage option"/>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	133 <param name="remove_dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False" label="Exclude reads marked as duplicates" help="--remove-dups; default = False"/>
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	134 <conditional name="split_output">
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	135 <param name="split_output_selector" type="select" label="Output" help="Select between a single output or separate outputs for each statistics">
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	136 <option value="no" selected="True">a single summary file</option>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	137 <option value="yes">separate datasets for each statistics</option>
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	138 </param>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	139 <when value="no" />
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	140 <when value="yes">
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	141 <param name="generate_tables" type="select" display="checkboxes" multiple="True" label="Statistics to extract">
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	142 <option value="sn">Summary numbers</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	143 <option value="ffq">First Fragment Qualities</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	144 <option value="lfq">Last Fragment Qualities</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	145 <option value="mpc">Mismatches per cycle</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	146 <option value="gcf">GC Content of first fragments</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	147 <option value="gcl">GC Content of last fragments</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	148 <option value="gcc">ACGT content per cycle</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	149 <option value="is">Insert sizes</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	150 <option value="rl">Read lengths</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	151 <option value="id">Indel distribution</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	152 <option value="ic">Indels per cycle</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	153 <option value="cov">Coverage distribution</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	154 <option value="gcd">GC depth</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	155 </param>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	156 </when>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	157 </conditional>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	158 <conditional name="filter_by_flags">
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	159 <param name="filter_flags" type="select" label="Set filter by flags" help="-f and -F options">
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	160 <option value="nofilter" selected="True">Do not filter</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	161 <option value="filter">Filter by flags to exclude or require</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	162 </param>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	163 <when value="filter">
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	164 <param name="require_flags" type="select" display="checkboxes" multiple="True" label="Require" help="-f">
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	165 <option value="1">Read is paired</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	166 <option value="2">Read is mapped in a proper pair</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	167 <option value="4">The read is unmapped</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	168 <option value="8">The mate is unmapped</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	169 <option value="16">Read strand</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	170 <option value="32">Mate strand</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	171 <option value="64">Read is the first in a pair</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	172 <option value="128">Read is the second in a pair</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	173 <option value="256">The alignment or this read is not primary</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	174 <option value="512">The read fails platform/vendor quality checks</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	175 <option value="1024">The read is a PCR or optical duplicate</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	176 </param>
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	177 <param name="exclude_flags" type="select" display="checkboxes" multiple="True" label="Exclude" help="-F">
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	178 <option value="1">Read is paired</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	179 <option value="2">Read is mapped in a proper pair</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	180 <option value="4">The read is unmapped</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	181 <option value="8">The mate is unmapped</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	182 <option value="16">Read strand</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	183 <option value="32">Mate strand</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	184 <option value="64">Read is the first in a pair</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	185 <option value="128">Read is the second in a pair</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	186 <option value="256">The alignment or this read is not primary</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	187 <option value="512">The read fails platform/vendor quality checks</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	188 <option value="1024">The read is a PCR or optical duplicate</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	189 </param>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	190 </when>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	191 <when value="nofilter" />
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	192
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	193 </conditional>
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	194 <param name="gc_depth" type="float" value="20000" label="GC-depth bin size" help="--GC-depth; decreasing bin size increases memory requirement; default = 20000.0"/>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	195 <param name="insert_size" type="integer" value="8000" label="Maximum insert size" help="--insert-size; default = 8000"/>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	196
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	197 <!--
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	198
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	199 The -I option of samtools stats returns the following message in version 1.2:
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	200
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	201 Samtools-htslib: init_group_id() header parsing not yet implemented
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	202 Abort trap: 6
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	203
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	204 Because of this the section below is commented out until this stats bug is fixed
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	205
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	206 <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" >
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	207 <options>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	208 <filter type="data_meta" ref="input_file" key="read_groups" />
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	209 </options>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	210 </param>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	211
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	212 -->
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	213
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	214 <param name="read_length" type="integer" value="0" label="Minimum read length to generate statistics for" help="--read-length; default = no cutoff"/>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	215 <param name="most_inserts" type="float" value="0.99" label="Report only the main part of inserts" help="--most-inserts; default = 0.99"/>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	216 <param name="trim_quality" type="integer" value="0" label="BWA trim parameter" help="--trim-quality; default = 0"/>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	217
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	218 <conditional name="use_reference">
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	219 <param name="use_ref_selector" type="select" label="Use reference sequence" help="--ref-seq; required for GC-depth and mismatches-per-cycle calculation">
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	220 <option value="yes">Use reference</option>
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	221 <option selected="True" value="no">Do not use reference</option>
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	222 </param>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	223 <when value="yes">
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	224 <conditional name="reference_source">
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	225 <param name="reference_source_selector" type="select" label="Choose a reference sequence for GC depth">
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	226 <option value="cached">Locally cached</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	227 <option value="history">History</option>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	228 </param>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	229 <when value="cached">
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	230 <param name="ref_file" type="select" label="Using genome">
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	231 <options from_data_table="fasta_indexes" />
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	232 <filter type="data_meta" ref="input_file" key="dbkey" column="1" />
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	233 </param>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	234 </when>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	235 <when value="history">
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	236 <param name="ref_file" type="data" format="fasta" label="Using file" />
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	237 </when>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	238 </conditional>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	239 </when>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	240 <when value="no" />
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	241 </conditional>
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	242
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	243 </inputs>
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	244
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	245 <outputs>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	246 <data format="tabular" name="output" label="${tool.name} on ${on_string}">
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	247 <discover_datasets pattern="(?P<designation>.+)\.tab" ext="tabular" visible="true" directory="split" />
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	248 </data>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	249 </outputs>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	250 <tests>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	251 <test>
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	252 <param name="input_file" value="samtools_stats_input.bam" ftype="bam" />
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	253 <param name="use_ref_selector" value="yes" />
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	254 <param name="reference_source_selector" value="history" />
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	255 <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" />
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	256 <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" />
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	257 </test>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	258 <test>
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	259 <param name="input_file" value="samtools_stats_input.bam" ftype="bam" />
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	260 <param name="use_ref_selector" value="yes" />
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	261 <param name="reference_source_selector" value="history" />
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	262 <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" />
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	263 <param name="split_output_selector" value="yes" />
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	264 <param name="generate_tables" value="sn,mpc,gcc" />
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	265 <output name="output" file="samtools_stats_out2.tab" lines_diff="4">
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	266 <discovered_dataset designation="Summary numbers" ftype="tabular" file="samtools_stats_out2/sn.tab" />
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	267 <discovered_dataset designation="ACGT content per cycle" ftype="tabular" file="samtools_stats_out2/gcc.tab" />
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	268 <discovered_dataset designation="Mismatches per cycle" ftype="tabular" file="samtools_stats_out2/mpc.tab" />
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	269 </output>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	270 </test>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	271 </tests>
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	272 <help><![CDATA[
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	273 What it does
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	274
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	275 This tool runs the ``samtools stats`` command. It has the following options::
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	276
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	277 -c, --coverage <int>,<int>,<int> Coverage distribution min,max,step [1,1000,1]
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	278 -d, --remove-dups Exclude from statistics reads marked as duplicates
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	279 -f, --required-flag <str\|int> Required flag, 0 for unset. See also `samtools flags` [0]
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	280 -F, --filtering-flag <str\|int> Filtering flag, 0 for unset. See also `samtools flags` [0]
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	281 --GC-depth <float> the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4]
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	282 -h, --help This help message
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	283 -i, --insert-size <int> Maximum insert size [8000]
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	284 -I, --id <string> Include only listed read group or sample name
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	285 -l, --read-length <int> Include in the statistics only reads with the given read length []
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	286 -m, --most-inserts <float> Report only the main part of inserts [0.99]
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	287 -q, --trim-quality <int> The BWA trimming parameter [0]
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	288 -r, --ref-seq <file> Reference sequence (required for GC-depth and mismatches-per-cycle calculation). Galaxy
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	289 will provide options for selecting a reference cached as this Galaxy instance or choosing
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	290 one from history.
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	291
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	292
1 cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	293 ]]></help>
cc56fc603e53 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	294 <expand macro="citations"></expand>
0 cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	295 </tool>
cd6eb75c9819 Uploaded initial tool definition. devteam parents: diff changeset	296

Mercurial > repos > devteam > samtools_stats

annotate samtools_stats.xml @ 2:b02596e3d7a3 draft