Mercurial > repos > iracooke > make_protein_decoys

annotate make_decoy.xml @ 3:84b15e316fcc draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 19:28:20 -0400
parents fa4ed0c996d9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
1 <tool id="make_decoy" name="Generate protein decoy sequences" version="1.0.1">
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
2 <description>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
3 Generate random protein sequences with the same AA composition as input sequences
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
4 </description>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
5 <requirements>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
6 <container type="docker">iracooke/protk-1.4.3</container>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
7 <requirement type="package" version="1.4.3">protk</requirement>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
8 </requirements>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
9 <stdio>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
10 <exit_code range="1:" level="fatal" description="Failure" />
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
11 </stdio>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
12 <command>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
13 make_decoy.rb $fasta_file -o $output -P $prefix_string $append
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
14 </command>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
15 <inputs>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
16 <param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" />
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
17 <param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
18 <param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" />
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
19 </inputs>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
20 <outputs>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
21 <data format="fasta" name="output" />
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
22 </outputs>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
23 <tests>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
24 <test>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
25 <param name="fasta_file" value="testdb.fasta" format="fasta"/>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
26 <output name="output" format="fasta">
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
27 <assert_contents>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
28 <has_text text="decoy_rp3" />
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
29 </assert_contents>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
30 </output>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
31 </test>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
32 </tests>
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
33 <help>
2
fa4ed0c996d9 Uploaded
iracooke
parents:
diff changeset
34
fa4ed0c996d9 Uploaded
iracooke
parents:
diff changeset
35 **What it does**
fa4ed0c996d9 Uploaded
iracooke
parents:
diff changeset
36
fa4ed0c996d9 Uploaded
iracooke
parents:
diff changeset
37 Generates random protein sequences based on the amino acid composition of a given set of input sequences. To be used for decoy proteomics searches
fa4ed0c996d9 Uploaded
iracooke
parents:
diff changeset
38
fa4ed0c996d9 Uploaded
iracooke
parents:
diff changeset
39
3
84b15e316fcc planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 2
diff changeset
40 </help>
2
fa4ed0c996d9 Uploaded
iracooke
parents:
diff changeset
41 </tool>