view spectrast2tsv.xml @ 0:e3a05965ca0c draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv commit d8b91dbe304c99bb5a46da25a5820005cde105c5-dirty

<tool id="gp_spectrast2tsv" name="Spectrast to TSV" version="0.1.0">
    <description>Filter from spectraST files to swath input files</description>
    <requirements>
        <requirement type="package" version="0.3.2">msproteomicstools</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <!-- In case the return code has not been set propery check stderr too -->
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <command>
<![CDATA[
        #set $input_files = list()
        #for $counter,$filename in enumerate($inputs):
            #set $tmp = "./%s.sptxt" % $counter;
            ln -s "$filename" "$tmp";
            #silent $input_files.append($tmp)
        #end for

        spectrast2tsv.py
            #if $fasta:
                -f ${fasta}
            #end if
            -a ${output}
            -q "\${GALAXY_SLOTS:-24}"
            $d
            $e
            -n $n
            -o $o
            #if $mass_modifs:
                -g "#echo ','.join([$param.mass_modif for $param in $mass_modifs])#"
            #end if
            -p $p
            #if $ion_series:
                -s "#echo ','.join([$param.ion for $param in $ion_series])#"
            #end if
            -t $time_scale
            #if $labeling_file:
                -i $labeling_file
            #end if
            -k $oformat
            #if $l_lower and $l_upper:
                -l "$l_lower,$l_upper"
            #end if
            #if $mods_file:
                -m $mods_file
            #end if
            #if $u:
                -u $u
            #end if
            #if $swaths_file:
                -w $swaths_file
            #end if
            -x "$x"
            -y $y
            #echo '" "'.join($input_files)#
]]>
    </command>
    <inputs>
        <param name="inputs" format="txt" type="data" multiple="True" label="Spectrast files" help="" />
        <param name="mods_file" format="txt" type="data" optional="True" label="File with the modifications delta mass" help="(-m)" />
        <param name="labeling_file" format="txt" type="data" optional="True"
            label="File containing the amino acid isotopic labeling mass shifts" help="If this option is used, heavy transitions will be generated. (-i)" />
        <param name="fasta" format="fasta" type="data" optional="True" label="Fasta file to relate peptides to their proteins" help="" />
        <param name="swaths_file" format="txt" type="data" optional="True"
            label="File containing the swath ranges" help="This is used to remove transitions with Q3 falling in the swath mass range. (-w)" />
        <param name="d" type="boolean" truevalue="-d" falsevalue="" checked="False"
            label="Remove duplicate masses from labeling" help="(-d)" />
        <param name="e" type="boolean" truevalue="-e" falsevalue="" checked="False"
            label="Use theoretical mass" help="(-e)" />
        <param name="o" type="integer" value="3" label="Min number of reported ions per peptide/z" help="(-o)" />
        <param name="n" type="integer" value="20" label="Max number of reported ions per peptide/z" help="(-n)" />

        <param name="l_lower" type="integer" optional="True" value="" label="Lower mass limit of fragment ions"
            help="You need to specify the upper limit as well, if you specify a lower limit. (-l)" />
        <param name="l_upper" type="integer" optional="True" value="" label="Upper mass limit of fragment ions"
            help="You need to specify the lower limit as well, if you specify a upper limit. (-l)" />

        <param name="u" type="integer" optional="True" value="" label="Use this unimod code as a switching modification" help="Useful for phosphorylations. (-u)" />

        <repeat name="mass_modifs" title="List of allowed fragment mass modifications"
            help="Useful for phosphorylation and neutral losses (-g)">
            <param name="mass_modif" type="float" value="" label="Fragment mass modifications" />
        </repeat>
        <param name="p" type="float" value="0.05" label="Maximum error allowed at the annotation of a fragment ion" help="(-p)" />

        <repeat name="ion_series" title="List of ion series to be used"
            help="(-s)">
            <param name="ion" type="text" value="" label="Ion series" />
        </repeat>
        <param name="time_scale" type="select" label="Time scale">
            <option value="minutes">Minutes</option>
            <option value="seconds" selected="True">Seconds</option>
        </param>
        <param name="oformat" type="select" label="Output format">
            <option value="openswath">OpenSwath</option>
            <option value="peakview" selected="True">Peakview</option>
        </param>
        <param name="x" type="text" value="1,2" label="Fragment ion charge states allowed" help="(-x)"/>
        <param name="y" type="integer" value="2"
            label="When using a switching modification, this determines the UIS order to be calculated"
            help="If -1 is set, all transitions for each isoform will be reported. (-y)" />

    </inputs>
    <outputs>
        <data format="tabular" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="inputs" value="testlib.sptxt" ftype="txt" />
            <param name="time_scale" value="minutes" />
            <param name="oformat" value="openswath" />
            <output name="output" file="spectrast2tsv_1_openswath_out.csv" ftype="tabular" />
        </test>
        <test>
            <param name="inputs" value="testlib.sptxt" ftype="txt" />
            <param name="labeling_file" value="labeling_file.txt" ftype="txt" />
            <param name="time_scale" value="minutes" />
            <param name="oformat" value="openswath" />
            <output name="output" file="spectrast2tsv_2_openswath_out.csv" ftype="tabular" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Filter from spectraST files to swath input files.


]]>
    </help>
    <citations>
    </citations>
</tool>