comparison dia_umpire_se.xml @ 1:acd0df26c1e9 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 73496bb9686e60f25d1cccf3410f1c53bf92d5f5-dirty

0:e8f7be6a6e59

&& cat $se_config > $se_params 
##
&& echo " " >> $se_params 
&& echo "Thread = \$GALAXY_SLOTS" >> $se_params
#if $input_prefix and len($input_prefix.strip()) > 0:
#set $input_path = $ser_dir + "/" + $input_prefix.__str__ + "_rep" + str($i + 1) + ".mzXML" 
#else:
#set $input_path = $ser_dir + "/" + $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input.name)) + ".mzXML"
#end if
&& ln -s '${input}' '$input_path'
&&  dia_umpire_se '$input_path' '$se_params'
&& cat $output_dir/*.log >> "$logfile"
#if not $mgfs_as_collection:
&& cp '$output_dir/*_Q1.mgf' '$q1_mgf'
&& cp '$output_dir/*_Q2.mgf' '$q2_mgf'
&& cp '$output_dir/*_Q3.mgf' '$q3_mgf'
#end if
]]>
    </command>
  <configfiles>
    <configfile name="se_config"><![CDATA[#slurp

               label="ExportPrecursorPeak"
               help="Output detailed information about detected MS1 precursor and MS2 unfragmented precursor signals"/>
        <param name="ExportFragmentPeak" type="boolean" truevalue="true" falsevalue="false" checked="false" 
               label="ExportFragmentPeak"
               help="Output detailed information about detected MS2 signals"/>
        <param name="se_extraction_data" type="boolean" truevalue="true" falsevalue="false" checked="false" 
               label="Output Signal Extraction data for DIA_Umpire_Quant" />
        <param name="mgfs_as_collection" type="boolean" truevalue="true" falsevalue="false" checked="false" 
               label="Output MGFs as a collection" />

    </inputs>

    <outputs>
        <data format="txt" name="logfile" label="${tool.name} log"/>
        <data format="dia_umpire.ser" name="se_params" label="${tool.name} Signal Extraction data">
            <filter>se_extraction_data</filter>
        </data>
        <data format="csv" name="PrecursorPeak" label="" from_work_dir="gx_path/swath_PeakCurve.csv">
            <filter>ExportPrecursorPeak</filter>
        </data>
        <data format="csv" name="FragmentPeak" label="" from_work_dir="gx_path/swath_PeakCurve.csv">
            <filter>ExportFragmentPeak</filter>
        </data>
        <collection name="dia_umpire_se_mgfs" type="list" label="${tool.name} MGFs">
            <filter>mgfs_as_collection</filter>
            <discover_datasets pattern="(?P&lt;name&gt;.*Q[1-3]\.mgf)" ext="mgf" visible="false" directory="gx_path" />
        </collection>
        <data format="csv" name="q1_mgf" label="${tool.name} Q1.mgf" >
            <filter>not mgfs_as_collection</filter>
        </data>
        <data format="csv" name="q2_mgf" label="${tool.name} Q2.mgf" >
            <filter>not mgfs_as_collection</filter>
        </data>
        <data format="csv" name="q3_mgf" label="${tool.name} Q3.mgf" >
            <filter>not mgfs_as_collection</filter>
        </data>
    </outputs>
    <tests>
        <test>

1:acd0df26c1e9

&& cat $se_config > $se_params 
##
&& echo " " >> $se_params 
&& echo "Thread = \$GALAXY_SLOTS" >> $se_params
#if $input_prefix and len($input_prefix.strip()) > 0:
#set $input_path = str($output_dir) + '/' + $input_prefix.__str__ + '_rep' + str($i + 1) + '.mzXML' 
#else:
#set $input_path = str($output_dir) + '/' + $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input.name)) + '.mzXML'
#end if
&& ln -s '${input}' '$input_path'
&&  dia_umpire_se '$input_path' '$se_params'
&& cat $output_dir/*.log >> "$logfile"
#if not $mgfs_as_collection:
&& cp "$output_dir/"*_Q1.mgf '$q1_mgf'
&& cp "$output_dir/"*_Q2.mgf '$q2_mgf'
&& cp "$output_dir/"*_Q3.mgf '$q3_mgf'
#end if
#if $ExportPrecursorPeak:
&& cp "$output_dir/"*PeakCluster.csv '$PrecursorPeak'
#end if
]]>
    </command>
  <configfiles>
    <configfile name="se_config"><![CDATA[#slurp

               label="ExportPrecursorPeak"
               help="Output detailed information about detected MS1 precursor and MS2 unfragmented precursor signals"/>
        <param name="ExportFragmentPeak" type="boolean" truevalue="true" falsevalue="false" checked="false" 
               label="ExportFragmentPeak"
               help="Output detailed information about detected MS2 signals"/>
        <param name="se_extraction_data" type="boolean" truevalue="Signal Extraction data" falsevalue="diaumpire_se.params" checked="false" 
               label="Output Signal Extraction data for DIA_Umpire_Quant" />
        <param name="mgfs_as_collection" type="boolean" truevalue="true" falsevalue="false" checked="false" 
               label="Output MGFs as a collection" />

    </inputs>

    <outputs>
        <data format="txt" name="logfile" label="${tool.name} ${on_string} log"/>
        <data format="dia_umpire.ser" name="se_params" label="${tool.name} ${input.name} ${se_extraction_data}">
        </data>
        <data format="csv" name="PrecursorPeak" label="${tool.name} ${input.name} PeakCluster.csv" from_work_dir="gx_path/swath_PeakCurve.csv">
            <filter>ExportPrecursorPeak</filter>
        </data>
        <!--
        <data format="csv" name="FragmentPeak" label="" from_work_dir="gx_path/swath_PeakCurve.csv">
            <filter>ExportFragmentPeak</filter>
        </data>
        -->
        <collection name="dia_umpire_se_mgfs" type="list" label="${tool.name} MGFs">
            <filter>mgfs_as_collection</filter>
            <discover_datasets pattern="(?P&lt;name&gt;.*Q[1-3]\.mgf)" ext="mgf" visible="false" directory="gx_path" />
        </collection>
        <data format="mgf" name="q1_mgf" label="${tool.name} ${input.name}_Q1.mgf" >
            <filter>not mgfs_as_collection</filter>
        </data>
        <data format="mgf" name="q2_mgf" label="${tool.name} ${input.name}_Q2.mgf" >
            <filter>not mgfs_as_collection</filter>
        </data>
        <data format="mgf" name="q3_mgf" label="${tool.name} ${input.name}_Q3.mgf" >
            <filter>not mgfs_as_collection</filter>
        </data>
    </outputs>
    <tests>
        <test>