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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author | iuc |
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date | Tue, 09 May 2017 11:18:11 -0400 |
parents | 1ebb4ecdc1ef |
children | e65c2cd0964c |
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<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 && #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> <inputs> <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> <option value="history">Use a genome from the history</option> </param> <when value="cached"> <param name="ref_fasta" type="select" label="Using reference genome"> <options from_data_table="fasta_indexes"> <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> </when> <when value="history"> <param name="ref_fasta" type="data" format="fasta" label="Using reference file" /> </when> </conditional> <conditional name="option_set"> <param name="option_sets" type="select" label="Options"> <option value="default">Use defaults</option> <option value="advanced">Advanced options</option> </param> <when value="default" /> <when value="advanced"> <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 name="calmd_output" format="bam" label="${tool.name} on ${on_string}" /> </outputs> <tests> <test> <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="change_identical" value="true" /> <param name="extended_baq" value="true" /> <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_2.bam" ftype="bam" /> </test> </tests> <help><![CDATA[ **What it does** 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. ----- **NM and MD tags** 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 references for more information about SAM format tags. ]]></help> <expand macro="citations"/> </tool>