comparison createDatabase.xml @ 14:64a315b27e1c draft default tip

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc

13:e1a2d0616d80

<tool id="mspurity_createdatabase" name="msPurity.createDatabase" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
    <description>
        Create and SQLite database of an LC-MS(/MS) experiment
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
	<requirement type="package" >libgfortran</requirement>
    </expand>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command interpreter="Rscript"><![CDATA[
        createDatabase.R
            --outDir=.
            --xset_xa=$xset_xa
	          --pa=$pa
            --xcms_camera_option=$camera_xcms
            --cores=\${GALAXY_SLOTS:-4}
            #if $file_load_conditional.file_load_select=="yes"
                --mzML_files='
                #for $i in $file_load_conditional.input

            #if $eic
                --eic
            #end if

            #if $grp_peaklist_opt.grp_peaklist_opt=="yes"
                --grp_peaklist=$grp_peaklist
            #end if

    ]]></command>
    <inputs>
        <param type="data" name="xset_xa" label="xcmsSet or CAMERA object"
               help="Either xcmsSet object saved as 'xset' or CAMERA 'xa' object in an RData file.
                     Please specify which to use below"
               format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/>
        <expand macro="camera_xcms" />
        <param type="data" name="pa" label="purityA object (frag4feature output)" format="rdata"
               help="purityA object saved as 'pa' in a RData file (output from frag4feature)"/>
      	<param name="eic" type="boolean" label="Include EIC data?"
               help="The Extracted Ion Chromatogram can be calculated for each peak and stored in
                     the database. Note, this will take considerable time for large datasets and
                     the resulting SQLite database can be large"/>
        <expand macro="grp_peaklist" />
          <expand macro="fileload" />
    </inputs>
    <outputs>
        <data name="createDatabase_output_sqlite" format="sqlite"
              label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db"
              from_work_dir="createDatabase_output.sqlite" />

14:64a315b27e1c

<tool id="mspurity_createdatabase" name="msPurity.createDatabase" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
    <description>Create and SQLite database of an LC-MS(/MS) experiment</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/createDatabase.R'
            --outDir=.
            --xset_xa='$xset_xa'
	          --pa='$pa'
            --xcms_camera_option=$camera_xcms
            --cores=\${GALAXY_SLOTS:-4}
            #if $file_load_conditional.file_load_select=="yes"
                --mzML_files='
                #for $i in $file_load_conditional.input

            #if $eic
                --eic
            #end if

            #if $grp_peaklist_opt.grp_peaklist_opt=="yes"
                --grp_peaklist='$grp_peaklist'
            #end if

    ]]></command>
    <inputs>
        <param argument="--xset_xa" type="data"  label="xcmsSet or CAMERA object"
               help="Either xcmsSet object saved as 'xset' or CAMERA 'xa' object in an RData file.
                     Please specify which to use below"
               format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/>
        <expand macro="camera_xcms" />
        <param argument="--pa" type="data" label="purityA object (frag4feature output)" format="rdata"
               help="purityA object saved as 'pa' in a RData file (output from frag4feature)"/>
      	<param argument="--eic" type="boolean" label="Include EIC data?"
               help="The Extracted Ion Chromatogram can be calculated for each peak and stored in
                     the database. Note, this will take considerable time for large datasets and
                     the resulting SQLite database can be large"/>
        <expand macro="grp_peaklist" />
        <expand macro="fileload" />
    </inputs>
    <outputs>
        <data name="createDatabase_output_sqlite" format="sqlite"
              label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db"
              from_work_dir="createDatabase_output.sqlite" />