annotate make_decoy.xml @ 3:255b5b6ec617 draft default tip

Better defaults for omssa
author Ira Cooke <iracooke@gmail.com>
date Mon, 23 Jul 2012 14:48:31 +1000
parents a929e27eb203
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
1 <tool id="make_decoy_1" name="Create decoy databases" version="1.0.0">
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
2 <requirements>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
3 <requirement type="package">protk</requirement>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
4 </requirements>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
5
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
6 <description>Creates a random protein database with similar properties to a real protein database</description>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
7
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
8 <command>make_decoy.rb $input_file -o $output -L $length -P $prefix $append</command>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
9
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
10 <inputs>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
11
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
12 <param name="input_file" type="data" format="fasta" multiple="false" label="Input File" help="Real protein sequences. Take care that these are fasta formatted with no more than 80 amino acids per line. There should be no whitespace in the sequences."/>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
13 <param name="prefix" type="text" label="String to prepend to generated protein ID's" size="60" value="decoy_"/>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
14 <param name="length" type="text" label="Number of random sequences to generate" help="If 0, a database of equal size to the input database will be generated" size="60" value="0"/>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
15 <param name="append" type="boolean" checked="true" label="Append input dataset to the generated sequences" truevalue="-A" falsevalue=""/>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
16 </inputs>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
17
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
18 <outputs>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
19 <data format="fasta" name="output" metadata_source="input_file" label="Random sequences from ${input_file.display_name}" from_work_dir="random.fasta"/>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
20 </outputs>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
21
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
22 <help>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
23 Create random protein sequences
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
24 </help>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
25
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
26 </tool>