Mercurial > repos > devteam > samtools_calmd
changeset 1:33208952b99d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
| author | iuc |
|---|---|
| date | Tue, 09 May 2017 11:18:11 -0400 |
| parents | 1ebb4ecdc1ef |
| children | e65c2cd0964c |
| files | macros.xml samtools_calmd.xml tool_dependencies.xml |
| diffstat | 3 files changed, 38 insertions(+), 46 deletions(-) [+] |
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--- a/macros.xml Tue Apr 21 15:13:37 2015 -0400 +++ b/macros.xml Tue May 09 11:18:11 2017 -0400 @@ -1,16 +1,17 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="1.3.1">samtools</requirement> <yield/> </requirements> </xml> + <token name="@TOOL_VERSION@">1.3.1</token> <xml name="citations"> <citations> <citation type="bibtex"> @misc{SAM_def, title={Definition of SAM/BAM format}, - url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + url = {https://samtools.github.io/hts-specs/},} </citation> <citation type="doi">10.1093/bioinformatics/btp352</citation> <citation type="doi">10.1093/bioinformatics/btr076</citation> @@ -41,7 +42,7 @@ </citations> </xml> <xml name="version_command"> - <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> </xml> <xml name="stdio"> <stdio> @@ -64,7 +65,5 @@ 5. Click **Save** The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. - </token> - </macros>
--- a/samtools_calmd.xml Tue Apr 21 15:13:37 2015 -0400 +++ b/samtools_calmd.xml Tue May 09 11:18:11 2017 -0400 @@ -1,26 +1,31 @@ -<tool id="samtools_calmd" name="CalMD" version="2.0"> - <description>recalculate MD/NM tags</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio"></expand> - <expand macro="version_command"></expand> +<tool id="samtools_calmd" name="CalMD" version="2.0.1"> + <description>recalculate MD/NM tags</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> <command><![CDATA[ #if str( $reference_source.reference_source_selector ) == "history": #set ref_fa = 'ref.fa' - ln -s "${reference_source.ref_fasta}" ref.fa && samtools faidx ref.fa && + ln -s '${reference_source.ref_fasta}' ref.fa && + samtools faidx ref.fa && #else: #set ref_fa = str( $reference_source.ref_fasta.fields.path ) #end if + samtools calmd - #if str($option_set.option_sets) == 'advanced': - $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq - #end if - -b "$input_bam" "$ref_fa" > "$calmd_output" ]]> - </command> + #if str($option_set.option_sets) == 'advanced': + $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq + #end if + -b + '$input_bam' + '$ref_fa' + > '$calmd_output' + ]]></command> <inputs> - <param format="bam" name="input_bam" type="data" label="BAM file to recalculate" /> + <param name="input_bam" type="data" format="bam" label="BAM file to recalculate" /> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> <option value="cached">Use a built-in genome</option> @@ -29,7 +34,7 @@ <when value="cached"> <param name="ref_fasta" type="select" label="Using reference genome"> <options from_data_table="fasta_indexes"> - <filter type="data_meta" column="0" key="dbkey" ref="input_bam" /> + <filter type="data_meta" column="1" key="dbkey" ref="input_bam" /> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> </options> </param> @@ -45,26 +50,26 @@ </param> <when value="default" /> <when value="advanced"> - <param name="change_identical" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" help="-e"/> - <param name="modify_quality" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" help="-A"/> - <param name="compute_cap" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" help="-r"/> - <param name="extended_baq" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" help="-E"/> + <param name="change_identical" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" /> + <param name="modify_quality" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" /> + <param name="compute_cap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" /> + <param name="extended_baq" argument="-E" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" /> </when> </conditional> </inputs> <outputs> - <data format="bam" name="calmd_output" label="${tool.name} on ${on_string}" /> + <data name="calmd_output" format="bam" label="${tool.name} on ${on_string}" /> </outputs> <tests> <test> - <param name="option_sets" value="default" /> + <param name="option_sets" value="default" /> <param name="input_bam" value="phiX.bam"/> <param name="reference_source_selector" value="history" /> <param name="ref_fasta" value="phiX.fasta" /> <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" /> </test> <test> - <param name="option_sets" value="advanced" /> + <param name="option_sets" value="advanced" /> <param name="change_identical" value="true" /> <param name="extended_baq" value="true" /> <param name="input_bam" value="phiX.bam"/> @@ -73,27 +78,21 @@ <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" /> </test> </tests> - <help> + <help><![CDATA[ **What it does** -Generates the MD tag using ``samtools calmd`` command. If the MD tag (see SAM format refernce below for explanation of SAM/BAM tags) is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file. The command has the following options:: +Generates the MD tag using the ``samtools calmd`` command. If the MD tag (see SAM format reference below for explanation of SAM/BAM tags) is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file. - -e change identical bases to '=' - -A modify the quality string - -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A) - -E extended BAQ for better sensitivity but lower specificity - ----- **NM and MD tags** -From SAM format specification:: +From the SAM format specification:: MD (string) String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7 NM (indeger) Edit distance to the reference, including ambiguous bases but excluding clipping - -See refernces for more information about SAM format tags. - </help> - <expand macro="citations"></expand> +See references for more information about SAM format tags. + ]]></help> + <expand macro="citations"/> </tool>
--- a/tool_dependencies.xml Tue Apr 21 15:13:37 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="samtools" version="1.2"> - <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>