| Previous changeset 10:3a0efe14891f (2022-06-22) Next changeset 12:541082d03bef (2024-09-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit cd62639660bef041ba14ecff337fb98e84e75d8a |
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modified:
macros.xml samtools_stats.xml |
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| diff -r 3a0efe14891f -r fed4aa48ba09 macros.xml --- a/macros.xml Wed Jun 22 07:48:55 2022 +0000 +++ b/macros.xml Mon Nov 20 22:17:08 2023 +0000 |
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| @@ -5,7 +5,14 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">1.13</token> + <!-- NOTE: for some tools only the version of the requirement but not the + tool's version is controlled by the TOOL_VERSION token + (because their version is ahead of the requirement version .. + please only bump the minor version in order to let the requirement + version catch up eventually). To find the tools check: + `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` --> + <token name="@TOOL_VERSION@">1.15.1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">20.05</token> <token name="@FLAGS@"><![CDATA[ #set $flags = 0 @@ -103,7 +110,7 @@ #end if ]]></token> - <xml name="optional_reference"> + <xml name="optional_reference" token_help="" token_argument=""> <conditional name="addref_cond"> <param name="addref_select" type="select" label="Use a reference sequence"> <help>@HELP@</help> @@ -212,37 +219,7 @@ <xml name="citations"> <citations> - <citation type="bibtex"> - @misc{SAM_def, - title={Definition of SAM/BAM format}, - url = {https://samtools.github.io/hts-specs/},} - </citation> - <citation type="doi">10.1093/bioinformatics/btp352</citation> - <citation type="doi">10.1093/bioinformatics/btr076</citation> - <citation type="doi">10.1093/bioinformatics/btr509</citation> - <citation type="bibtex"> - @misc{Danecek_et_al, - Author={Danecek, P., Schiffels, S., Durbin, R.}, - title={Multiallelic calling model in bcftools (-m)}, - url = {http://samtools.github.io/bcftools/call-m.pdf},} - </citation> - <citation type="bibtex"> - @misc{Durbin_VCQC, - Author={Durbin, R.}, - title={Segregation based metric for variant call QC}, - url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} - </citation> - <citation type="bibtex"> - @misc{Li_SamMath, - Author={Li, H.}, - title={Mathematical Notes on SAMtools Algorithms}, - url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} - </citation> - <citation type="bibtex"> - @misc{SamTools_github, - title={SAMTools GitHub page}, - url = {https://github.com/samtools/samtools},} - </citation> + <citation type="doi">10.1093/gigascience/giab008</citation> </citations> </xml> <xml name="version_command"> |
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| diff -r 3a0efe14891f -r fed4aa48ba09 samtools_stats.xml --- a/samtools_stats.xml Wed Jun 22 07:48:55 2022 +0000 +++ b/samtools_stats.xml Mon Nov 20 22:17:08 2023 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="samtools_stats" name="Samtools stats" version="2.0.4" profile="@PROFILE@">\n+<tool id="samtools_stats" name="Samtools stats" version="2.0.5" profile="@PROFILE@">\n <description>generate statistics for BAM dataset</description>\n <macros>\n <import>macros.xml</import>\n@@ -45,7 +45,7 @@\n #if $use_ref:\n --ref-seq "\\$reffa"\n #end if\n- ## TODO currently not implemented in Galaxy\n+ ## currently not implemented in Galaxy\n ## generates STR_VALUE.bamstat where STR is given by -P and VALUE is a value of the TAG given by -S\n ## needs some discover data sets action...\n ## -P, --split-prefix STR\n@@ -84,7 +84,7 @@\n <param name="coverage_step" type="integer" value="1" label="Coverage step" help="Step value for coverage" />\n </when>\n </conditional>\n- <param name="remove_dups" argument="--remove-dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False" label="Exclude reads marked as duplicates" />\n+ <param argument="--remove-dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False" label="Exclude reads marked as duplicates" />\n <conditional name="split_output_cond">\n <param name="split_output_selector" type="select" label="Output" help="Select between one single output or separate outputs for each statistics">\n <option value="no" selected="True">One single summary file</option>\n@@ -131,16 +131,16 @@\n </conditional>\n <!-- 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 -->\n <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" />\n- <param name="insert_size" argument="--insert-size" type="integer" optional="True" label="Maximum insert size" help="default=8000" />\n+ <param argument="--insert-size" type="integer" optional="True" label="Maximum insert size" help="default=8000" />\n <!-- TOOD https://github.com/samtools/samtools/issues/1489 --> \n <param name="read_group" argument="--id" type="select" optional="true" label="Limit to a specific read group name" >\n <options>\n <filter type="data_meta" ref="input" key="read_groups" />\n </options>\n </param>\n- <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" />\n- <param name="most_inserts" argument="--most-inserts" type="float" optional="true" label="Report only the main part of inserts" help="default=0.99" />\n- <param name="trim_quality" argument="--trim-quality" type="integer" optional="true" label="BWA trim parameter" help="default=0" />\n+ <param argument="--read-length" type="integer" optional="true" label="Minimum read length to generate statistics for" help="No cutoff if left empty" />\n+ <param argument="--most-inserts" type="float" optional="true" label="Report only the main part of inserts" help="default=0.99" />\n+ <param argument="--trim-quality" type="integer" optional="true" label="BWA trim parameter" help="default=0" />\n \n <expand macro="optional_reference" argument="--ref-seq" help="Required for GC-depth and mismatches-per-cycle calculation"/>\n <!-- unfortunately -t takes tabular and not bed like view (otherwise a macro might have simplified this) -->\n@@ -153,18 +153,17 @@\n </inputs>\n \n <outputs>\n- <data name="output" format="tabular" label="${tool.name} on ${on_string}">\n- <discover_datasets directory="split" pattern="(?P<designation>.+)\\.tab" format="tabular" vi'..b'" ftype="sam" />\n <conditional name="addref_cond">\n <param name="addref_select" value="no" />\n@@ -240,7 +239,7 @@\n <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/11.stats.g4.expected\',cmd=>"$$opts{bin}/samtools stats -g 4 -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix);-->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="11_target.bam" ftype="bam" />\n <conditional name="addref_cond">\n <param name="addref_select" value="no" />\n@@ -255,7 +254,7 @@\n <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/11.stats.g4.expected\',cmd=>"$$opts{bin}/samtools stats -g 4 $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix); -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="12_overlaps.bam" ftype="bam" />\n <conditional name="addref_cond">\n <param name="addref_select" value="no" />\n@@ -267,7 +266,7 @@\n <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="4" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/12.3reads.overlap.expected\',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="12_overlaps.bam" ftype="bam" />\n <conditional name="addref_cond">\n <param name="addref_select" value="no" />\n@@ -280,7 +279,7 @@\n <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="4" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/12.3reads.nooverlap.expected\',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="12_overlaps.bam" ftype="bam" />\n <conditional name="addref_cond">\n <param name="addref_select" value="no" />\n@@ -292,7 +291,7 @@\n <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="4" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/12.2reads.overlap.expected\',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="12_overlaps.bam" ftype="bam" />\n <conditional name="addref_cond">\n <param name="addref_select" value="no" />\n@@ -305,7 +304,7 @@\n <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="4" />\n </test>\n <!-- test_cmd($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);-->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="samtools_stats_input.bam" ftype="bam" />\n <conditional name="addref_cond">\n <param name="addref_select" value="history" />\n@@ -313,7 +312,7 @@\n </conditional>\n <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" />\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="samtools_stats_input.bam" ftype="bam" />\n <conditional name="addref_cond">\n <param name="addref_select" value="history" />\n' |