Mercurial > repos > devteam > samtools_stats
diff 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 |
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--- a/samtools_stats.xml Thu Oct 17 02:21:23 2019 -0400 +++ b/samtools_stats.xml Tue Sep 28 16:17:39 2021 +0000 @@ -1,4 +1,4 @@ -<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> @@ -16,16 +16,12 @@ #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 - @FLAGS@ - --required-flag $flags - #end if - #if $filter_by_flags.exclude_flags: - #set $filter = $filter_by_flags.exclude_flags - @FLAGS@ - --filtering-flag $flags - #end if + #set $filter = $filter_by_flags.require_flags + @FLAGS@ + --required-flag $flags + #set $filter = $filter_by_flags.exclude_flags + @FLAGS@ + --filtering-flag $flags #end if #if str($gc_depth): --GC-depth ${gc_depth} @@ -33,12 +29,9 @@ #if str($insert_size): --insert-size ${insert_size} #end if - ## The code below is commented out because using -I/--id options causes - ## in samtools up to 1.9 the following exception - ## Samtools-htslib: init_group_id() header parsing not yet implemented - ##if str($read_group) != "": - ## -I "${read_group}" - ##end if + ## #if $read_group + ## -I '$read_group' + ## #end if #if str($read_length): --read-length ${read_length} #end if @@ -63,7 +56,7 @@ #if str($cov_threshold): -g $cov_threshold #end if - -@ \$addthreads + -@ \$addthreads infile @REGIONS_MANUAL@ > '$output' @@ -139,40 +132,19 @@ <!-- 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" /> - <!-- - The -I option of samtools stats returns the following message up to version 1.9: - Samtools-htslib: init_group_id() header parsing not yet implemented - Because of this the section below is commented out until this stats bug is fixed - <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" > - <options> - <filter type="data_meta" ref="input" key="read_groups" /> - </options> - </param> - --> + <!-- TOOD https://github.com/samtools/samtools/issues/1489 --> + <param name="read_group" argument="--id" type="select" optional="true" label="Limit to a specific read group name" > + <options> + <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"> - <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> + <expand macro="optional_reference" argument="--ref-seq" help="Required for GC-depth and mismatches-per-cycle calculation"/> <!-- 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."/> @@ -198,7 +170,7 @@ <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 $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix);--> <test> @@ -207,7 +179,7 @@ <param name="addref_select" value="history" /> <param name="ref" value="test.fa" ftype="fasta" /> </conditional> - <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="3" /> + <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="2" /> </test> <!-- test_cmd($opts,out=>'stat/2.stats.expected',cmd=>"$$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 $$opts{path}/stat/3_map_cigar_equal_seq.sam | tail -n+4", exp_fix=>$efix);--> @@ -220,7 +192,7 @@ <param name="addref_select" value="history" /> <param name="ref" value="test.fa" ftype="fasta" /> </conditional> - <output name="output" file="6.stats.expected" ftype="tabular" lines_diff="3" /> + <output name="output" file="6.stats.expected" ftype="tabular" lines_diff="2" /> </test> <!-- test_cmd($opts,out=>'stat/6.stats.expected',cmd=>"$$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 $$opts{path}/stat/7_supp.sam | tail -n+4", exp_fix=>$efix); --> @@ -236,7 +208,7 @@ <param name="select_region" value="tab"/> <param name="targetregions" value="11.stats.targets" ftype="tabular" /> </conditional> - <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="3" /> + <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="4" /> </test> <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix); --> @@ -251,7 +223,7 @@ <param name="regions_repeat_1|region" value="ref1:30-46"/> <param name="regions_repeat_2|region" value="ref1:39-56"/> </conditional> - <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="3" /> + <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="2" /> </test> <!-- test_cmd($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=>$efix); --> @@ -265,7 +237,7 @@ <param name="targetregions" value="11.stats.targets" ftype="tabular" /> </conditional> <param name="cov_threshold" value="4" /> - <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="3" /> + <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" /> </test> <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix);--> <test> @@ -280,7 +252,7 @@ <param name="regions_repeat_2|region" value="ref1:39-56"/> </conditional> <param name="cov_threshold" value="4" /> - <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="3" /> + <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="2" /> </test> <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix); --> <test> @@ -292,7 +264,7 @@ <param name="select_region" value="tab"/> <param name="targetregions" value="12_3reads.bed" ftype="tabular" /> </conditional> - <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="3" /> + <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="4" /> </test> <!-- test_cmd($opts,out=>'stat/12.3reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);--> <test> @@ -305,7 +277,7 @@ <param name="targetregions" value="12_3reads.bed" ftype="tabular" /> </conditional> <param name="remove_overlaps" value="-p"/> - <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="3" /> + <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="4" /> </test> <!-- test_cmd($opts,out=>'stat/12.3reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);--> <test> @@ -317,7 +289,7 @@ <param name="select_region" value="tab"/> <param name="targetregions" value="12_2reads.bed" ftype="tabular" /> </conditional> - <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="3" /> + <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="4" /> </test> <!-- test_cmd($opts,out=>'stat/12.2reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);--> <test> @@ -330,7 +302,7 @@ <param name="targetregions" value="12_2reads.bed" ftype="tabular" /> </conditional> <param name="remove_overlaps" value="-p"/> - <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="3" /> + <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="4" /> </test> <!-- test_cmd($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> @@ -357,6 +329,18 @@ <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** @@ -367,4 +351,3 @@ ]]></help> <expand macro="citations"/> </tool> -