Mercurial > repos > galaxyp > ms_wiff_loader
diff ms_wiff_loader.xml @ 0:5bc64a2d5f91 draft default tip
Uploaded
| author | galaxyp |
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| date | Tue, 10 Mar 2015 18:26:36 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ms_wiff_loader.xml Tue Mar 10 18:26:36 2015 -0400 @@ -0,0 +1,45 @@ +<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>