Mercurial > repos > iracooke > tpp_prophets

annotate pepxml_to_table.xml @ 17:868e75fc0f70 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Export XML_ONLY variable
author iracooke
date Mon, 26 Oct 2015 22:04:43 -0400
parents 1b86e378de37
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
15
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
1 <tool id="pepxml_to_table_1" name="PepXML to Table" version="1.1.1">
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
2 <description>Converts a pepXML file to a tab delimited text file</description>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
3 <requirements>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
4 <container type="docker">iracooke/protk-1.4.3</container>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
5 <requirement type="package" version="1.4.3">protk</requirement>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
6 </requirements>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
7 <!-- Note .. the input file is assumed to be the first argument -->
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
8 <command>pepxml_to_table.rb $input_file -o $output $invert_probs</command>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
9 <inputs>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
10 <param name="input_file" type="data" format="pepxml,raw_pepxml,peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Input File" help="A pepXML file"/>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
11 <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
12 </inputs>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
13 <outputs>
16
1b86e378de37 Fix tabular outputs. Export XML_ONLY variable
iracooke
parents: 15
diff changeset
14 <data format="tabular" name="output" metadata_source="input_file" label="${input_file.display_name}.tsv" />
15
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
15 </outputs>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
16 <tests>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
17 <!-- Just test that the tool runs and produces vaguely correct output -->
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
18 <test>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
19 <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml" format="raw_pepxml"/>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
20 <output name="output" format="csv">
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
21 <assert_contents>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
22 <has_text text="ANTNNYAPKSSR" />
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
23 </assert_contents>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
24 </output>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
25 </test>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
26 </tests>
12
4c66453a168e Uploaded
iracooke
parents:
diff changeset
27 <help>
15
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
diff changeset
28 Convert a pepXML file to Tab delimited text
12
4c66453a168e Uploaded
iracooke
parents:
diff changeset
29 </help>
4c66453a168e Uploaded
iracooke
parents:
diff changeset
30 </tool>