comparison hicBuildMatrix.xml @ 7:be42758f532e draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01

6:30d427846764

<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.1">
    <description>creates a contact matrix</description>
    <macros>
        <token name="@BINARY@">hicBuildMatrix</token>
        <import>macros.xml</import>
    </macros>

            #if $region:
                --region '$region'
            #end if

            #if $outputFormat == 'h5'
                --outFileName matrix.h5
            #elif $outputFormat == 'cool'
                --outFileName matrix.cool
            #end if
            --outBam ./unsorted.bam

            $keepSelfCircles

            #if $minMappingQuality and $minMappingQuality is not None:

        &&
        mv ./QCfolder/* $qc.files_path/
        &&
        mv $qc.files_path/hicQC.html $qc
        && mv $qc.files_path/*.log raw_qc
        && samtools sort ./unsorted.bam -o sorted.bam
       
]]>
    </command>
    <inputs>

            <option value="cool">cool</option>
        </param>
    </inputs>
    <outputs>
        <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
        <data name="outFileName_h5" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}">
            <filter>outputFormat == 'h5'</filter>
        </data>
        <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool" label="${tool.name} MATRIX on ${on_string}">
            <filter>outputFormat == 'cool'</filter>
        </data>
        <data name="qc" format="html" label="${tool.name} QC"/>
        <data name="raw_qc" from_work_dir='raw_qc' label="${tool.name} raw QC" />
    </outputs>
    <tests>
        <test>
            <repeat name="samFiles">
                <param name="samFile" value="small_test_R1_unsorted.sam"/>

                <param name="binSize" value="5000"/>
            </conditional>
            <param name='outputFormat' value='h5'/>

            <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
            <output name="outFileName_h5" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/>
            <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
        </test>
    </tests>
    <help><![CDATA[

- long range

Read orientation:
_________________
- inward pairs
- outward pairs
- left pairs
- right pairs 

.. image:: $PATH_TO_IMAGES/hicQC.png
   :width: 70 %

7:be42758f532e

<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.2">
    <description>creates a contact matrix</description>
    <macros>
        <token name="@BINARY@">hicBuildMatrix</token>
        <import>macros.xml</import>
    </macros>

            #if $region:
                --region '$region'
            #end if

            --outFileName matrix.$outputFormat
        
            --outBam ./unsorted.bam

            $keepSelfCircles

            #if $minMappingQuality and $minMappingQuality is not None:

        &&
        mv ./QCfolder/* $qc.files_path/
        &&
        mv $qc.files_path/hicQC.html $qc
        && mv $qc.files_path/*.log raw_qc
        && mv matrix.$outputFormat matrix
        && samtools sort ./unsorted.bam -o sorted.bam
       
]]>
    </command>
    <inputs>

            <option value="cool">cool</option>
        </param>
    </inputs>
    <outputs>
        <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
        <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
            <change_format>
                <when input="outputFormat" value="cool" format="cool" />
            </change_format>
        </data>
        <data name="qc" format="html" label="${tool.name} QC"/>

        <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC" />
    </outputs>
    <tests>
        <test>
            <repeat name="samFiles">
                <param name="samFile" value="small_test_R1_unsorted.sam"/>

                <param name="binSize" value="5000"/>
            </conditional>
            <param name='outputFormat' value='h5'/>

            <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
            <output name="outFileName" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/>
            <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
        </test>
    </tests>
    <help><![CDATA[

- long range

Read orientation:
_________________
- inward pairs
- outward pairs 
- left pairs
- right pairs 

.. image:: $PATH_TO_IMAGES/hicQC.png
   :width: 70 %