annotate rmats.xml @ 0:ff15d6def09b draft

"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 315f6ba609e9545c3a374f7fd471aee50b135ec8-dirty"

<tool id="rmats" name="rMats turbo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
    <description>detect differential alternative splicing events from RNA-Seq</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        echo $b1 > b1.txt &&
        #if $b2
          echo $b2 > b2.txt &&
        #end if
        rmats.py 
        --b1 b1.txt
        #if $b2
          --b1 b1.txt
        #end if
        --gtf '$gtf'
        #if $novel.novelSS == 'yes'
            --novelSS
            #if $novel.mil
              --mil $novel.mil
            #end if
            #if $novel.mel
              --mel $novel.mel
            #end if
        #end if
        #if $readLength
          --readLength $readLength
        #end if
        $variable_read_length
        #if $libType
          --libType "$libType"
        #end if
        #if $anchorLength
          --anchorLength $anchorLength
        #end if
        #if $cstat
          --cstat $cstat
        #end if
        $paired_stats
        --nthread \${GALAXY_SLOTS:-1}
        --tmp tmp
        --od outputs
    ]]></command>
    <inputs>
        <param name="b1" type="data" format="bam" multiple="true" label="BAM files for sample_1"/>
        <param name="b2" type="data" format="bam" multiple="true" optional="true" label="BAM files for sample_2"/>
        <param name="gtf" type="data" format="gtf" label="GTF - annotation of genes and transcripts"/>

        <conditional name="novel">
            <param name="novelSS" argument="--novelSS" type="select" label="Enable detection of novel splice sites">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param argument="--mil" type="integer" value="" optional="true" label="Minimum Intron Length" help=" Default is 50"/>
                <param argument="--mel" type="integer" value="" optional="true" label="Maximum Exon Length" help=" Default is 500"/>
            </when> 
        </conditional>
        <param argument="--readLength" type="integer" value="150" label="The length of each read"/>
        <param name="variable_read_length" argument="--variable-read-length" type="boolean" truevalue="--variable-read-length" falsevalue="" checked="true" label="Allow reads with lengths that differ from --readLength to be processed"/>

        <param argument="--libType" type="select" optional="true" label="Library type" 
            help="Use fr-firststrand or fr-secondstrand for strand-specific data. Default: fr-unstranded">
            <option value="fr-unstranded">fr-unstranded</option>
            <option value="fr-firststrand">fr-firststrand</option>
            <option value="fr-secondstrand">fr-secondstrand</option>
        </param>

        <param argument="--anchorLength" type="integer" value="" optional="true" label="The anchor length" help=" Default is 1"/>

        <param argument="--cstat" type="float" value="" min="0." max="1." optional="true" label="The cutoff splicing difference." help="The cutoff used in the null hypothesis test for differential splicing. The default is 0.0001 for 0.01% difference. Does not apply to the paired stats model"/>
        <param name="paired_stats" argument="--paired-stats" type="boolean" truevalue="--paired-stats" falsevalue="" checked="true" label="Enable detection of novel splice sites"/>
        
        <param name="history_outputs" type="select" multiple="true" label="Select outputs">
            <option value="SE.MATS.JC.txt">SE.MATS.JC.txt</option>
            <option value="SE.MATS.JCEC.txt">SE.MATS.JCEC.txt</option>
            <option value="MXE.MATS.JC.txt">MXE.MATS.JC.txt</option>
            <option value="MXE.MATS.JCEC.txt">MXE.MATS.JCEC.txt</option>
            <option value="A3SS.MATS.JC.txt">A3SS.MATS.JC.txt</option>
            <option value="A3SS.MATS.JCEC.txt">A3SS.MATS.JCEC.txt</option>
            <option value="A5SS.MATS.JC.txt">A5SS.MATS.JC.txt</option>
            <option value="A5SS.MATS.JCEC.txt">A5SS.MATS.JCEC.txt</option>
            <option value="RI.MATS.JC.txt">RI.MATS.JC.txt</option>
            <option value="RI.MATS.JCEC.txt">RI.MATS.JCEC.txt</option>
            <option value="fromGTF.SE.txt">fromGTF.SE.txt</option>
            <option value="fromGTF.novelJunction.SE.txt">fromGTF.novelJunction.SE.txt</option>
            <option value="fromGTF.novelSpliceSite.SE.txt">fromGTF.novelSpliceSite.SE.txt</option>
            <option value="fromGTF.MXE.txt">fromGTF.MXE.txt</option>
            <option value="fromGTF.novelJunction.MXE.txt">fromGTF.novelJunction.MXE.txt</option>
            <option value="fromGTF.novelSpliceSite.MXE.txt">fromGTF.novelSpliceSite.MXE.txt</option>
            <option value="fromGTF.A3SS.txt">fromGTF.A3SS.txt</option>
            <option value="fromGTF.novelJunction.A3SS.txt">fromGTF.novelJunction.A3SS.txt</option>
            <option value="fromGTF.novelSpliceSite.A3SS.txt">fromGTF.novelSpliceSite.A3SS.txt</option>
            <option value="fromGTF.A5SS.txt">fromGTF.A5SS.txt</option>
            <option value="fromGTF.novelJunction.A5SS.txt">fromGTF.novelJunction.A5SS.txt</option>
            <option value="fromGTF.novelSpliceSite.A5SS.txt">fromGTF.novelSpliceSite.A5SS.txt</option>
            <option value="fromGTF.RI.txt">fromGTF.RI.txt</option>
            <option value="fromGTF.novelJunction.RI.txt">fromGTF.novelJunction.RI.txt</option>
            <option value="fromGTF.novelSpliceSite.RI.txt">fromGTF.novelSpliceSite.RI.txt</option>
        </param> 
        
    </inputs>
    <outputs>
        <data name="summary" format="tabular" label="${tool.name} on ${on_string}: summary.txt" from_work_dir="outputs/summary.txt">
            <expand macro="output_actions" column_names="@COLNAME_SUMMARY@"/>
        </data>

        <data name="fromGTF_SE" format="tabular" label="${tool.name} on ${on_string}: fromGTF.SE.txt" from_work_dir="outputs/fromGTF.SE.txt">
            <filter>history_outputs and 'fromGTF.SE.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_SE_GTF@"/>
        </data>
        <data name="fromGTF_A3SS" format="tabular" label="${tool.name} on ${on_string}: fromGTF.A3SS.txt" from_work_dir="outputs/fromGTF.A3SS.txt">
            <filter>history_outputs and 'fromGTF.A3SS.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_A_SS_GTF@"/>
        </data>
        <data name="fromGTF_A5SS" format="tabular" label="${tool.name} on ${on_string}: fromGTF.A5SS.txt" from_work_dir="outputs/fromGTF.A5SS.txt">
            <filter>history_outputs and 'fromGTF.A5SS.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_A_SS_GTF@"/>
        </data>
        <data name="fromGTF_MXE" format="tabular" label="${tool.name} on ${on_string}: fromGTF.MXE.txt" from_work_dir="outputs/fromGTF.MXE.txt">
            <filter>history_outputs and 'fromGTF.MXE.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_MXE_GTF@"/>
        </data>
        <data name="fromGTF_RI" format="tabular" label="${tool.name} on ${on_string}: fromGTF.RI.txt" from_work_dir="outputs/fromGTF.RI.txt">
            <filter>history_outputs and 'fromGTF.RI.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_RI_GTF@"/>
        </data>

        <data name="fromGTF_novelSpliceSite_SE" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelSpliceSite.SE.txt" from_work_dir="outputs/fromGTF.novelSpliceSite.SE.txt">
            <filter>history_outputs and 'fromGTF.novelSpliceSite.SE.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_SE_GTF@"/>
        </data>
        <data name="fromGTF_novelSpliceSite_A3SS" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelSpliceSite.A3SS.txt" from_work_dir="outputs/fromGTF.novelSpliceSite.A3SS.txt">
            <filter>history_outputs and 'fromGTF.novelSpliceSite.A3SS.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_A_SS_GTF@"/>
        </data>
        <data name="fromGTF_novelSpliceSite_A5SS" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelSpliceSite.A5SS.txt" from_work_dir="outputs/fromGTF.novelSpliceSite.A5SS.txt">
            <filter>history_outputs and 'fromGTF.novelSpliceSite.A5SS.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_A_SS_GTF@"/>
        </data>
        <data name="fromGTF_novelSpliceSite_MXE" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelSpliceSite.MXE.txt" from_work_dir="outputs/fromGTF.novelSpliceSite.MXE.txt">
            <filter>history_outputs and 'fromGTF.novelSpliceSite.MXE.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_MXE_GTF@"/>
        </data>
        <data name="fromGTF_novelSpliceSite_RI" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelSpliceSite.RI.txt" from_work_dir="outputs/fromGTF.novelSpliceSite.RI.txt">
            <filter>history_outputs and 'fromGTF.novelSpliceSite.RI.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_RI_GTF@"/>
        </data>

        <data name="fromGTF_novelJunction_SE" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelJunction.SE.txt" from_work_dir="outputs/fromGTF.novelJunction.SE.txt">
            <filter>history_outputs and 'fromGTF.novelJunction.SE.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_SE_GTF@"/>
        </data>
        <data name="fromGTF_novelJunction_A3SS" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelJunction.A3SS.txt" from_work_dir="outputs/fromGTF.novelJunction.A3SS.txt">
            <filter>history_outputs and 'fromGTF.novelJunction.A3SS.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_A_SS_GTF@"/>
        </data>
        <data name="fromGTF_novelJunction_A5SS" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelJunction.A5SS.txt" from_work_dir="outputs/fromGTF.novelJunction.A5SS.txt">
            <filter>history_outputs and 'fromGTF.novelJunction.A5SS.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_A_SS_GTF@"/>
        </data>
        <data name="fromGTF_novelJunction_MXE" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelJunction.MXE.txt" from_work_dir="outputs/fromGTF.novelJunction.MXE.txt">
            <filter>history_outputs and 'fromGTF.novelJunction.MXE.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_MXE_GTF@"/>
        </data>
        <data name="fromGTF_novelJunction_RI" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelJunction.RI.txt" from_work_dir="outputs/fromGTF.novelJunction.RI.txt">
            <filter>history_outputs and 'fromGTF.novelJunction.RI.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_RI_GTF@"/>
        </data>

        <data name="SE_MATS_JCEC" format="tabular" label="${tool.name} on ${on_string}: SE.MATS.JCEC.txt" from_work_dir="outputs/SE.MATS.JCEC.txt">
            <filter>history_outputs and 'SE.MATS.JCEC.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_SE@"/>
        </data>
        <data name="SE_MATS_JC" format="tabular" label="${tool.name} on ${on_string}: SE.MATS.JC.txt" from_work_dir="outputs/SE.MATS.JC.txt">
            <filter>history_outputs and 'SE.MATS.JC.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_SE@"/>
        </data>
        <data name="A3SS_MATS_JCEC" format="tabular" label="${tool.name} on ${on_string}: A3SS.MATS.JCEC.txt" from_work_dir="outputs/A3SS.MATS.JCEC.txt">
            <filter>history_outputs and 'A3SS.MATS.JCEC.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_A_SS@"/>
        </data>
        <data name="A3SS_MATS_JC" format="tabular" label="${tool.name} on ${on_string}: A3SS.MATS.JC.txt" from_work_dir="outputs/A3SS.MATS.JC.txt">
            <filter>history_outputs and 'A3SS.MATS.JC.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_A_SS@"/>
        </data>
        <data name="A5SS_MATS_JCEC" format="tabular" label="${tool.name} on ${on_string}: A5SS.MATS.JCEC.txt" from_work_dir="outputs/A5SS.MATS.JCEC.txt">
            <filter>history_outputs and 'A5SS.MATS.JCEC.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_A_SS@"/>
        </data>
        <data name="A5SS_MATS_JC" format="tabular" label="${tool.name} on ${on_string}: A5SS.MATS.JC.txt" from_work_dir="outputs/A5SS.MATS.JC.txt">
            <filter>history_outputs and 'A5SS.MATS.JC.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_A_SS@"/>
        </data>
        <data name="MXE_MATS_JCEC" format="tabular" label="${tool.name} on ${on_string}: MXE.MATS.JCEC.txt" from_work_dir="outputs/MXE.MATS.JCEC.txt">
            <filter>history_outputs and 'MXE.MATS.JCEC.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_MXE@"/>
        </data>
        <data name="MXE_MATS_JC" format="tabular" label="${tool.name} on ${on_string}: MXE.MATS.JC.txt" from_work_dir="outputs/MXE.MATS.JC.txt">
            <filter>history_outputs and 'MXE.MATS.JC.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_MXE@"/>
        </data>
        <data name="RI_MATS_JCEC" format="tabular" label="${tool.name} on ${on_string}: RI.MATS.JCEC.txt" from_work_dir="outputs/RI.MATS.JCEC.txt">
            <filter>history_outputs and 'RI.MATS.JCEC.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_RI@"/>
        </data>
        <data name="RI_MATS_JC" format="tabular" label="${tool.name} on ${on_string}: RI.MATS.JC.txt" from_work_dir="outputs/RI.MATS.JC.txt">
            <filter>history_outputs and 'RI.MATS.JC.txt' in history_outputs</filter>
            <expand macro="output_actions" column_names="@COLNAMES_RI@"/>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="b1" ftype="bam" value="normal_small.bam"/>
            <param name="b2" ftype="bam" value="cancer_small.bam"/>
            <param name="gtf" ftype="gtf" value="GRCh38.gtf"/>
            <param name="readLength" value="150"/>
            <param name="variable_read_length" value="True"/>
            <output name="summary" file="out/summary.txt" ftype="tabular"/>
        </test>

        <test>
            <param name="b1" ftype="bam" value="normal_small.bam"/>
            <param name="b2" ftype="bam" value="cancer_small.bam"/>
            <param name="gtf" ftype="gtf" value="GRCh38.gtf"/>
            <param name="readLength" value="150"/>
            <param name="variable_read_length" value="True"/>
            <conditional name="novel">
                <param name="novelSS" value="yes"/>
                <param name="mil" value="40"/>
            </conditional> 
            <output name="summary" file="novel/summary.txt" ftype="tabular"/>
        </test>

        <test>
            <param name="b1" ftype="bam" value="normal_small.bam"/>
            <param name="b2" ftype="bam" value="cancer_small.bam"/>
            <param name="gtf" ftype="gtf" value="GRCh38.gtf"/>
            <param name="readLength" value="150"/>
            <param name="variable_read_length" value="True"/>
            <conditional name="novel">
                <param name="novelSS" value="yes"/>
            </conditional> 
            <param name="paired_stats" value="True"/>
            <param name="" value="SE.MATS.JC.txt,MXE.MATS.JC.txt"/>
            <output name="summary">
                <assert_contents>
                    <has_text_matching expression="EventType"/>
                </assert_contents>
            </output>
            <output name="summary" file="novel/summary.txt" ftype="tabular"/>
        </test>

    </tests>
    <help><![CDATA[
** rMATS **

RMATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design.

https://github.com/Xinglab/rmats-turbo#starting-with-bam-files

https://github.com/Xinglab/rmats-turbo#output

    ]]></help>
    <expand macro="citations" />
</tool>