annotate scaffold_export.xml @ 0:e9981e6af666 draft

Improved some datatype handling

<tool id="scaffold_export" name="Scaffold Export" version="0.1.0">
  <description>
    Export summary from Scaffold SF3 file.
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <command interpreter="python">
    scaffold_wrapper.py export \
    --sf3 $sf3_input \
    --output $output \
    --export_type $export.export_type \
    ## Begin Threshold Parameters
    #set $threshold_type = $threshold.type
    #set $threshold_options = $threshold
    #if $threshold_type != "none"
    --protein_probability=$threshold_options.protein_probability \
    --peptide_probability=$threshold_options.peptide_probability \
    --minimum_peptide_count=$threshold_options.minimum_peptide_count \
    #if $threshold_type != "simple"
    $threshold_options.ignore_charge_1 \
    $threshold_options.ignore_charge_2 \
    $threshold_options.ignore_charge_3 \
    $threshold_options.ignore_charge_4 \
    --minimum_ntt=$threshold_options.minimum_ntt \
    --minimum_peptide_length=$threshold_options.minimum_peptide_length \
    #end if
    #end if
    ## End Threshold Parameters
  </command>
  <inputs>
    <param format="sf3" name="sf3_input" type="data" label="Scaffold Results" />
    <conditional name="export">
      <param name="export_type" type="select" label="Export Format">
        <option value="mzIdentML">MzIdentML</option>
        <option value="protxml">ProtXML</option>
        <option value="statistics">Stastics (tabular)</option>
        <option value="spectrum-report">Spectrum Report (tabular)</option>
        <option value="peptide-report">Peptide Report (tabular)</option>
        <option value="protein-report">Protein Report (tabular)</option>
        <option value="publication-report">Publication Report (tabular)</option>
        <option value="isoform-report">Isoform Report (tabular)</option>
        <option value="spectrum-counting-report">Spectrum Counting Report (tabular)</option>
        <option value="accession-report">Accession Report (tabular)</option>
        <option value="experiment-report">Experiment Report (tabular)</option>
      </param>
    </conditional>
    <expand macro="threshold" />
  </inputs>
  <outputs>
    <data format="tabular" name="output">
      <change_format>
        <when input="export.export_type" value="mzIdentML" format="mzid" />
        <when input="export.export_type" value="protxml" format="protxml" />
      </change_format>
    </data>
  </outputs>
  <requirements>
    <requirement type="package">scaffold</requirement>
  </requirements>
  <help>
**What it does**

Export data out of Scaffold's binary data format (sf3) into tabular reports or XML.

------


**Citation**

For the underlying tool, please cite `TODO`

If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-scaffold
  </help>
</tool>