annotate ms_wiff_loader.xml @ 0:5bc64a2d5f91 draft default tip

Uploaded

<tool id="ms_wiff_upload" name="MS Wiff Upload" version="1.0.0">
  <description>into a galaxy dataset</description>
  <stdio>
    <exit_code range="1:" err_level="fatal" />
  </stdio>
  <command interpreter="python">ms_wiff_loader.py -w "$wiff" 
  #if len(str($scan)) > 0:
    -s "$scan"
  #end if
  #if len(str($mtd)) > 0:
    -m "$mtd"
  #end if
  -f "$out_file"
  -o "${out_file.extra_files_path}"
  </command>
  <inputs>
    <param name="wiff" type="text" value="" size="120" label="URL to .wiff file">
      <validator type="regex" message="Must be a URL">^(ftp://|http://|https://|file:/)?(\\d+\\.\\d+\\.\\d+\\.\\d+|localhost|[a-zA-Z][^/]+)(:\\d+)?/(.*)$</validator>
    </param>
    <param name="scan" type="text" value="" size="120" label="URL to .wiff.scan file (optional)" optional="true">
      <validator type="regex" message="Must be a URL">^(ftp://|http://|https://|file:/)?(\\d+\\.\\d+\\.\\d+\\.\\d+|localhost|[a-zA-Z][^/]+)(:\\d+)?/(.*)$</validator>
    </param>
    <param name="mtd" type="text" value="" size="120" label="URL to .wiff.mtd file (optional)" optional="true">
      <validator type="regex" message="Must be a URL">^(ftp://|http://|https://|file:/)?(\\d+\\.\\d+\\.\\d+\\.\\d+|localhost|[a-zA-Z][^/]+)(:\\d+)?/(.*)$</validator>
    </param>
    <param name="name" type="text" value="" size="40" label="Name for dataset (optional)" optional="true">
    </param>
  </inputs>
  <outputs>
    <data format="wiff" name="out_file" label="$name wiff"/>
  </outputs>
  <tests>
    <test>
      <param name="wiff" value="http://www.ebi.ac.uk/pride/data/archive/2015/01/PXD001010/nselevse_L120327_016.wiff"/>
      <output name="out_file">
        <assert_contents>
          <has_text text="Wiff" />
        </assert_contents>
      </output>
    </test>
  </tests>
<help>
Loads AB SCIEX wiff files into a Galaxy Composite dataset.
</help>
</tool>