Mercurial > repos > iuc > reprof

comparison reprof.xml @ 3:8a1cd8a32a72 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reprof commit 746aa691891448484ef9f6417c708b6c7e8f60b0
author iuc
date Wed, 02 Dec 2015 16:34:05 -0500
parents 141da185be70
children 5a02100f8f6e
comparison
equal deleted inserted replaced
2:ae7de35846d8 3:8a1cd8a32a72
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 ##if str($query.ext) == 'pssm':
10 ##end if
11
12 ln -s $query query.fa; 9 ln -s $query query.fa;
13 python $__tool_directory__/reprof.py query.fa $REPROF_MODEL_DIR 10 python $__tool_directory__/reprof.py query.fa $REPROF_MODEL_DIR
14 ]]></command> 11 ]]></command>
15 <inputs> 12 <inputs>
16 <param name="query" label="Protein sequences" type="data" format="fasta" /> 13 <param name="query" label="Protein sequences" type="data" format="fasta" />
14 <param name="outputs" type="select" multiple="true" label="Additional Outputs">
15 <option value="pE">Probability of Extended/Sheet</option>
16 <option value="pH">Probability of Helix</option>
17 <option value="pL">Probability of Loop</option>
18 <option value="RI_S">Secondary Structure Reliability Index</option>
19
20 <option value="PACC">Absolute Solvent Accessibility</option>
21 <option value="PREL">Relative Solvent Accessibility</option>
22 <option value="P10">Relative Solvent Accessibility</option>
23 <option value="RI_A">Solvent Accessibility Reliability Index</option>
24 </param>
17 </inputs> 25 </inputs>
18 <outputs> 26 <outputs>
19 <data format="gff3" name="secondary_structure" from_work_dir="secondary_structure.gff3" label="Secondary Structure of ${on_string}"/> 27 <data format="gff3" name="secondary_structure" from_work_dir="secondary_structure.gff3" label="Secondary Structure of ${on_string}"/>
20 <data format="wig" name="pE" from_work_dir="pE.wig" label="Probability of Extended/Sheet (${on_string})"/> 28 <data format="wig" name="pE" from_work_dir="pE.wig" label="Probability of Extended/Sheet (${on_string})">
21 <data format="wig" name="pH" from_work_dir="pH.wig" label="Probability of Helix (${on_string})" /> 29 <filter>'pE' in outputs</filter>
22 <data format="wig" name="pL" from_work_dir="pL.wig" label="Probability of Loop (${on_string})" /> 30 </data>
23 <data format="wig" name="RI_S" from_work_dir="RI_S.wig" label="Secondary Structure Reliability Index (${on_string})"/> 31 <data format="wig" name="pH" from_work_dir="pH.wig" label="Probability of Helix (${on_string})">
32 <filter>'pH' in outputs</filter>
33 </data>
34 <data format="wig" name="pL" from_work_dir="pL.wig" label="Probability of Loop (${on_string})" >
35 <filter>'pL' in outputs</filter>
36 </data>
37 <data format="wig" name="RI_S" from_work_dir="RI_S.wig" label="Secondary Structure Reliability Index (${on_string})">
38 <filter>'RI_S' in outputs</filter>
39 </data>
24 40
25 <data format="gff3" name="solvent_accessibility" from_work_dir="solvent_accessibility.gff3" label="Solvent Accessibile Regions of ${on_string}" /> 41 <data format="gff3" name="solvent_accessibility" from_work_dir="solvent_accessibility.gff3" label="Solvent Accessibile Regions of ${on_string}" />
26 <data format="wig" name="PACC" from_work_dir="PACC.wig" label="Absolute Solvent Accessibility of ${on_string}"/> 42 <data format="wig" name="PACC" from_work_dir="PACC.wig" label="Absolute Solvent Accessibility of ${on_string}">
27 <data format="wig" name="PREL" from_work_dir="PREL.wig" label="Relative Solvent Accessibility of ${on_string}"/> 43 <filter>'PACC' in outputs</filter>
28 <data format="wig" name="P10" from_work_dir="P10.wig" label="Relative Solvent Accessibility (0-9) of ${on_string}"/> 44 </data>
29 <data format="wig" name="RI_A" from_work_dir="RI_A.wig" label="Solvent Accessibility Reliability Index (${on_string})"/> 45 <data format="wig" name="PREL" from_work_dir="PREL.wig" label="Relative Solvent Accessibility of ${on_string}">
46 <filter>'PREL' in outputs</filter>
47 </data>
48 <data format="wig" name="P10" from_work_dir="P10.wig" label="Relative Solvent Accessibility (0-9) of ${on_string}">
49 <filter>'P10' in outputs</filter>
50 </data>
51 <data format="wig" name="RI_A" from_work_dir="RI_A.wig" label="Solvent Accessibility Reliability Index (${on_string})">
52 <filter>'RI_A' in outputs</filter>
53 </data>
30 </outputs> 54 </outputs>
31 <tests> 55 <tests>
32 <test> 56 <test>
33 <param name="query" value="test.fa" /> 57 <param name="query" value="test.fa" />
34 58