Mercurial > repos > peterjc > clinod
comparison tools/clinod/clinod.xml @ 7:f61366a4a14e draft
v0.0.10 Internal changes to command line handling
author | peterjc |
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date | Tue, 16 May 2017 08:50:43 -0400 |
parents | 77cfe958b5ea |
children | 4863b1dbe8f0 |
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6:77cfe958b5ea | 7:f61366a4a14e |
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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> |