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comparison tools/clinod/clinod.xml @ 7:f61366a4a14e draft

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v0.0.10 Internal changes to command line handling
author peterjc
date Tue, 16 May 2017 08:50:43 -0400
parents 77cfe958b5ea
children 4863b1dbe8f0
comparison
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6:77cfe958b5ea 7:f61366a4a14e
1 <tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.9"> 1 <tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.10">
2 <description>Find nucleolar localization signals (NoLSs) in protein sequences</description> 2 <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
3 <requirements> 3 <requirements>
4 <requirement type="binary">java</requirement>
5 <requirement type="package" version="1.3">clinod</requirement> 4 <requirement type="package" version="1.3">clinod</requirement>
6 </requirements> 5 </requirements>
7 <stdio>
8 <!-- Assume anything other than zero is an error -->
9 <exit_code range="1:" />
10 <exit_code range=":-1" />
11 </stdio>
12 <version_command> 6 <version_command>
13 ##The first non-blank line contains the version information, e.g. 7 ##The first non-blank line contains the version information, e.g.
14 ##NucleOlar localization sequence Detector v. 1.3b (13 May 2011) 8 ##NucleOlar localization sequence Detector v. 1.3b (13 May 2011)
15 ##Question: Why don't we have to escape the dollar here? 9 ##Question: Why don't we have to escape the dollar here?
16 java -jar $CLINOD/clinod-1.3.jar | grep -i "^NucleOlar localization sequence Detector" 10 java -jar $CLINOD/clinod-1.3.jar | grep -i "^NucleOlar localization sequence Detector"
17 </version_command> 11 </version_command>
18 <command> 12 <command detect_errors="aggressive">
19 ##The Galaxy Tool Shed installation should define $CLINOD to point at folder 13 ##The Galaxy Tool Shed installation should define $CLINOD to point at folder
20 ##containing both clinod-1.3.jar and the batchman binary: 14 ##containing both clinod-1.3.jar and the batchman binary:
21 java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t="\$GALAXY_SLOTS" -f=MEDIUM_TAB -nonols -clean_sequence 15 java -jar \$CLINOD/clinod-1.3.jar -in='$fasta_file' -out='$tabular_file' -t="\${GALAXY_SLOTS:-4}" -f=MEDIUM_TAB -nonols -clean_sequence
22 ##TODO - Make the -clean_sequence argument a parameter? 16 ##TODO - Make the -clean_sequence argument a parameter?
23 </command> 17 </command>
24 <inputs> 18 <inputs>
25 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 19 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
26 </inputs> 20 </inputs>