samtools_stats: samtools_stats.xml comparison

comparison samtools_stats.xml @ 8:e28839a4b932 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"

author	iuc
date	Tue, 28 Sep 2021 16:17:39 +0000
parents	145f6d74ff5e
children	1cc79f49b8d5

comparison

equal deleted inserted replaced

-:145f6d74ff5e
+:e28839a4b932
-<tool id="samtools_stats" name="Samtools stats" version="2.0.2+galaxy2">
+<tool id="samtools_stats" name="Samtools stats" version="2.0.3" profile="@PROFILE@">
 <description>generate statistics for BAM dataset</description>
 <macros>
 <import>macros.xml</import>
 </macros>
 <expand macro="requirements"/>
 #if $coverage_cond.coverage_select == 'yes':
 --coverage ${coverage_cond.coverage_min},${coverage_cond.coverage_max},${coverage_cond.coverage_step}
 #end if
 ${remove_dups}
 #if str( $filter_by_flags.filter_flags ) == "filter":
-#if $filter_by_flags.require_flags:
+#set $filter = $filter_by_flags.require_flags
-#set $filter = $filter_by_flags.require_flags
+@FLAGS@
-@FLAGS@
+--required-flag $flags
---required-flag $flags
+#set $filter = $filter_by_flags.exclude_flags
-#end if
+@FLAGS@
-#if $filter_by_flags.exclude_flags:
+--filtering-flag $flags
-#set $filter = $filter_by_flags.exclude_flags
-@FLAGS@
---filtering-flag $flags
-#end if
 #end if
 #if str($gc_depth):
 --GC-depth ${gc_depth}
 #end if
 #if str($insert_size):
 --insert-size ${insert_size}
 #end if
-## The code below is commented out because using -I/--id options causes
+## #if $read_group
-## in samtools up to 1.9 the following exception
+##    -I '$read_group'
-## Samtools-htslib: init_group_id() header parsing not yet implemented
+## #end if
-##if str($read_group) != "":
-##    -I "${read_group}"
-##end if
 #if str($read_length):
 --read-length ${read_length}
 #end if
 #if str($most_inserts):
 --most-inserts ${most_inserts}
 @REGIONS_FILE@
 $remove_overlaps
 #if str($cov_threshold):
 -g $cov_threshold
 #end if
 -@ \$addthreads
 infile
 @REGIONS_MANUAL@
 > '$output'
 #if $split_output_cond.split_output_selector == "yes":
 </conditional>
 <!-- TODO I would like to set the default values of float and int parameters as on the samtools stats help page, but then the tests don't work. Hence I leave the optional and give the defaults in the help -->
 <param name="gc_depth" argument="--GC-depth" type="float" optional="True" label="Size of GC-depth bins" help="Decreasing bin size increases memory requirement. default=2e4" />
 <param name="insert_size" argument="--insert-size" type="integer" optional="True" label="Maximum insert size" help="default=8000" />
-<!--
+<!-- TOOD https://github.com/samtools/samtools/issues/1489 -->
-The -I option of samtools stats returns the following message up to version 1.9:
+<param name="read_group" argument="--id" type="select" optional="true" label="Limit to a specific read group name" >
-Samtools-htslib: init_group_id() header parsing not yet implemented
+<options>
-Because of this the section below is commented out until this stats bug is fixed
+<filter type="data_meta" ref="input" key="read_groups" />
-<param name="read_group" type="select" optional="true" label="Limit to a specific read group name" >
+</options>
-<options>
+</param>
-<filter type="data_meta" ref="input" key="read_groups" />
-</options>
-</param>
--->
 <param name="read_length" argument="--read-length" type="integer" optional="true" label="Minimum read length to generate statistics for" help="No cutoff if left empty" />
 <param name="most_inserts" argument="--most-inserts" type="float" optional="true" label="Report only the main part of inserts" help="default=0.99" />
 <param name="trim_quality" argument="--trim-quality" type="integer" optional="true" label="BWA trim parameter" help="default=0" />
-<conditional name="addref_cond">
+<expand macro="optional_reference" argument="--ref-seq" help="Required for GC-depth and mismatches-per-cycle calculation"/>
-<param name="addref_select" type="select" label="Use a reference sequence" help="Required for GC-depth and mismatches-per-cycle calculation">
-<option value="no">No</option>
-<option value="cached">Locally cached</option>
-<option value="history">History</option>
-</param>
-<when value="no"/>
-<when value="cached">
-<param name="ref" type="select" label="Using genome">
-<options from_data_table="fasta_indexes">
-<filter type="data_meta" ref="input" key="dbkey" column="dbkey" />
-</options>
-</param>
-</when>
-<when value="history">
-<param name="ref" type="data" format="fasta" label="Using file" />
-</when>
-</conditional>
 <!-- unfortunately -t takes tabular and not bed like view (otherwise a macro might have simplified this) -->
 <expand macro="regions_macro"/>
 <param name="sparse" argument="-x/--sparse" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Suppress absence of insertions" help="Suppress outputting IS rows where there are no insertions."/>
 <param name="remove_overlaps" argument="-p/--remove-overlaps" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Remove overlaps of paired-end reads from coverage and base count computations" />
 <param name="cov_threshold" argument="-g/--cov-threshold"  optional="true" type="integer" label="Only bases with coverage above this value will be included in the target percentage computation" />
 <param name="input" value="1_map_cigar.sam" ftype="sam" />
 <conditional name="addref_cond">
 <param name="addref_select" value="history" />
 <param name="ref" value="test.fa" ftype="fasta" />
 </conditional>
-<output name="output" file="1.stats.expected" ftype="tabular" lines_diff="3" />
+<output name="output" file="1.stats.expected" ftype="tabular" lines_diff="2" />
 </test>
 <!-- test_cmd($opts,out=>'stat/1.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix);-->
 <test>
 <param name="input" value="2_equal_cigar_full_seq.sam" ftype="sam" />
 <conditional name="addref_cond">
 <param name="addref_select" value="history" />
 <param name="ref" value="test.fa" ftype="fasta" />
 </conditional>
-<output name="output" file="2.stats.expected" ftype="tabular" lines_diff="3" />
+<output name="output" file="2.stats.expected" ftype="tabular" lines_diff="2" />
 </test>
 <!-- test_cmd($opts,out=>'stat/2.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/2_equal_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);-->
 <!-- test_cmd($opts,out=>'stat/3.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/3_map_cigar_equal_seq.sam | tail -n+4", exp_fix=>$efix);-->
 <!-- test_cmd($opts,out=>'stat/4.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/4_X_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);-->
 <!-- test_cmd($opts,out=>'stat/5.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); -->
 <param name="insert_size" value="0" />
 <conditional name="addref_cond">
 <param name="addref_select" value="history" />
 <param name="ref" value="test.fa" ftype="fasta" />
 </conditional>
-<output name="output" file="6.stats.expected" ftype="tabular" lines_diff="3" />
+<output name="output" file="6.stats.expected" ftype="tabular" lines_diff="2" />
 </test>
 <!-- test_cmd($opts,out=>'stat/6.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa -i 0 $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); -->
 <!-- test_cmd($opts,out=>'stat/7.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/7_supp.sam | tail -n+4", exp_fix=>$efix); -->
 <!-- test_cmd($opts,out=>'stat/8.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/8_secondary.sam | tail -n+4", exp_fix=>$efix);-->
 <!-- test_cmd($opts,out=>'stat/9.stats.expected',cmd=>"$$opts{bin}/samtools stats -S RG -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix,out_map=>{"stat/1_map_cigar.sam_s1_a_1.bamstat"=>"stat/1_map_cigar.sam_s1_a_1.expected.bamstat"},hskip=>3);-->
 </conditional>
 <conditional name="cond_region">
 <param name="select_region" value="tab"/>
 <param name="targetregions" value="11.stats.targets" ftype="tabular" />
 </conditional>
-<output name="output" file="11.stats.expected" ftype="tabular" lines_diff="3" />
+<output name="output" file="11.stats.expected" ftype="tabular" lines_diff="4" />
 </test>
 <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix); -->
 <test>
 <param name="input" value="11_target.bam" ftype="bam" />
 <param name="select_region" value="text"/>
 <param name="regions_repeat_0|region" value="ref1:10-24"/>
 <param name="regions_repeat_1|region" value="ref1:30-46"/>
 <param name="regions_repeat_2|region" value="ref1:39-56"/>
 </conditional>
-<output name="output" file="11.stats.expected" ftype="tabular" lines_diff="3" />
+<output name="output" file="11.stats.expected" ftype="tabular" lines_diff="2" />
 </test>
 <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix);
 -->
 <test>
 <param name="input" value="11_target.sam" ftype="sam" />
 <conditional name="cond_region">
 <param name="select_region" value="tab"/>
 <param name="targetregions" value="11.stats.targets" ftype="tabular" />
 </conditional>
 <param name="cov_threshold" value="4" />
-<output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="3" />
+<output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" />
 </test>
 <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix);-->
 <test>
 <param name="input" value="11_target.bam" ftype="bam" />
 <conditional name="addref_cond">
 <param name="regions_repeat_0|region" value="ref1:10-24"/>
 <param name="regions_repeat_1|region" value="ref1:30-46"/>
 <param name="regions_repeat_2|region" value="ref1:39-56"/>
 </conditional>
 <param name="cov_threshold" value="4" />
-<output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="3" />
+<output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="2" />
 </test>
 <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix); -->
 <test>
 <param name="input" value="12_overlaps.bam" ftype="bam" />
 <conditional name="addref_cond">
 </conditional>
 <conditional name="cond_region">
 <param name="select_region" value="tab"/>
 <param name="targetregions" value="12_3reads.bed" ftype="tabular" />
 </conditional>
-<output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="3" />
+<output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="4" />
 </test>
 <!-- test_cmd($opts,out=>'stat/12.3reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->
 <test>
 <param name="input" value="12_overlaps.bam" ftype="bam" />
 <conditional name="addref_cond">
 <conditional name="cond_region">
 <param name="select_region" value="tab"/>
 <param name="targetregions" value="12_3reads.bed" ftype="tabular" />
 </conditional>
 <param name="remove_overlaps" value="-p"/>
-<output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="3" />
+<output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
 </test>
 <!-- test_cmd($opts,out=>'stat/12.3reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->
 <test>
 <param name="input" value="12_overlaps.bam" ftype="bam" />
 <conditional name="addref_cond">
 </conditional>
 <conditional name="cond_region">
 <param name="select_region" value="tab"/>
 <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
 </conditional>
-<output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="3" />
+<output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="4" />
 </test>
 <!-- test_cmd($opts,out=>'stat/12.2reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
 <test>
 <param name="input" value="12_overlaps.bam" ftype="bam" />
 <conditional name="addref_cond">
 <conditional name="cond_region">
 <param name="select_region" value="tab"/>
 <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
 </conditional>
 <param name="remove_overlaps" value="-p"/>
-<output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="3" />
+<output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
 </test>
 <!-- test_cmd($opts,out=>'stat/12.2reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
 <test>
 <param name="input" value="samtools_stats_input.bam" ftype="bam" />
 <conditional name="addref_cond">
 <element name="ACGT content per cycle" ftype="tabular" file="samtools_stats_out1__gcc.tab"/>
 <element name="Mismatches per cycle and quality" ftype="tabular" file="samtools_stats_out1__mpc.tab" />
 <element name="Summary Numbers" ftype="tabular" file="samtools_stats_out1__sn.tab" />
 </output_collection>
 </test>
+<!-- test filtering by read group -->
+<!-- <test>
+<param name="input" value="11_target.sam" ftype="sam" />
+<conditional name="addref_cond">
+<param name="addref_select" value="no" />
+</conditional>
+<param name="read_group" value="grp1" />
+<output name="output" file="11.stats.read_groups.expected" ftype="tabular" lines_diff="2" />
+<assert_command>
+<has_text text="-I 'grp1'"/>
+</assert_command>
+</test> -->
 </tests>
 <help><![CDATA[
 **What it does**
 This tool runs the ``samtools stats`` command.
 The results of samtools stats can be visualized with MultiQC (for this the default of a single output file needs to be selected).
 ]]></help>
 <expand macro="citations"/>
 </tool>

Mercurial > repos > devteam > samtools_stats

comparison samtools_stats.xml @ 8:e28839a4b932 draft