comparison samtools_calmd.xml @ 5:c147e3a10573 draft

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

4:06dc50b7b711

<tool id="samtools_calmd" name="CalMD" version="2.0.2">
    <description>recalculate MD/NM tags</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@ADDTHREADS@
#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
    $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq
    #if str($option_set.option_sets) == 'advanced':
        $option_set.change_identical -C $option_set.adjust_mq
    #end if
    -b
    -@ \$addthreads
    '$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="dbkey" 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="baq_settings">
            <param name="use_baq" argument="-r" type="select"
            label="Do you also want BAQ (Base Alignment Quality) scores to be calculated?">
                <option value="">No</option>
                <option value="-r">Yes, run BAQ calculation</option>

    </outputs>
    <tests>
        <test>
            <param name="use_baq" value="" />
            <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="use_baq" value="-r" />
            <param name="extended_baq" value="true" />
            <param name="option_sets" value="advanced" />
            <param name="change_identical" value="true" />
            <param name="adjust_mq" value="50" />
            <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**

From the SAM format tag specification::

  MD (string)  String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7
  NM (integer) Edit distance to the reference, including ambiguous bases but excluding clipping
  BQ (string)  String of offsets to base alignment quality (BAQ), of the same length as the read sequence. 
               At the i-th read base, BAQ i = Q i − (BQ i − 64) where Q i is the i-th base quality.

See references for more information about SAM format tags.
    ]]></help>
    <expand macro="citations"/>

5:c147e3a10573

<tool id="samtools_calmd" name="Samtools calmd" version="2.0.3" profile="@PROFILE@">
    <description>recalculate MD/NM tags</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@ADDTHREADS@
@PREPARE_FASTA_IDX@

samtools calmd
    $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq
    #if str($option_set.option_sets) == 'advanced':
        $option_set.change_identical -C $option_set.adjust_mq
    #end if
    -b
    -@ \$addthreads
    '$input'
    '$reffa'
    > '$calmd_output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="bam" label="BAM file to recalculate" />
        <expand macro="mandatory_reference"/>
        <conditional name="baq_settings">
            <param name="use_baq" argument="-r" type="select"
            label="Do you also want BAQ (Base Alignment Quality) scores to be calculated?">
                <option value="">No</option>
                <option value="-r">Yes, run BAQ calculation</option>

    </outputs>
    <tests>
        <test>
            <param name="use_baq" value="" />
            <param name="option_sets" value="default" />
            <param name="input" value="phiX.bam"/>
            <param name="addref_select" value="history" />
            <param name="ref" value="phiX.fasta" />
            <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" lines_diff="4" />
        </test>
        <test>
            <param name="use_baq" value="-r" />
            <param name="extended_baq" value="true" />
            <param name="option_sets" value="advanced" />
            <param name="change_identical" value="true" />
            <param name="adjust_mq" value="50" />
            <param name="input" value="phiX.bam"/>
            <param name="addref_select" value="history" />
            <param name="ref" value="phiX.fasta" />
            <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" lines_diff="4" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

From the SAM format tag specification::

  MD (string)  String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7
  NM (integer) Edit distance to the reference, including ambiguous bases but excluding clipping
  BQ (string)  String of offsets to base alignment quality (BAQ), of the same length as the read sequence.
               At the i-th read base, BAQ i = Q i − (BQ i − 64) where Q i is the i-th base quality.

See references for more information about SAM format tags.
    ]]></help>
    <expand macro="citations"/>