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comparison readseq.xml @ 4:1a40d002fdc4 draft default tip

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planemo upload
author gandres
date Wed, 15 Jun 2016 09:18:26 -0400
parents b38275a23ce0
children
comparison
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3:b38275a23ce0 4:1a40d002fdc4
1 <tool id="sniplay_readseq" name="Readseq" version="1.0.2"> 1 <tool id="sniplay_readseq" name="Readseq" version="1.0.3">
2 2
3 <!-- [REQUIRED] Tool description displayed after the tool name --> 3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description> Convert various alignment formats </description> 4 <description> Convert various alignment formats </description>
5 5
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> 6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
15 <exit_code range="1:" level="fatal" /> 15 <exit_code range="1:" level="fatal" />
16 </stdio> 16 </stdio>
17 17
18 <!-- [REQUIRED] The command to execute --> 18 <!-- [REQUIRED] The command to execute -->
19 <command> 19 <command>
20 echo \$JAVA_JAR_PATH &amp;&amp;
21 java -jar \$JAVA_JAR_PATH/readseq.jar $filein -f $format >> $fileout_log 2>&amp;1 &amp;&amp; 20 java -jar \$JAVA_JAR_PATH/readseq.jar $filein -f $format >> $fileout_log 2>&amp;1 &amp;&amp;
22 #if str( $format ) == "1": 21 #if str( $format ) == "1":
23 mv ${filein}.ig $fileout 22 mv ${filein}.ig $fileout
24 #elif str( $format ) == "2" : 23 #elif str( $format ) == "2" :
25 mv ${filein}.gb $fileout 24 mv ${filein}.gb $fileout
82 </inputs> 81 </inputs>
83 82
84 <!-- [REQUIRED] Output files --> 83 <!-- [REQUIRED] Output files -->
85 <outputs> 84 <outputs>
86 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> 85 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
87 <data name="fileout" type="data" format="txt" label="${fileout_label}" /> 86 <data name="fileout" type="data" format="txt" label="${fileout_label}" >
87 <change_format>
88 <when input="format" value="1" format="ig" />
89 <when input="format" value="2" format="genbank" />
90 <when input="format" value="4" format="embl" />
91 <when input="format" value="5" format="gcg" />
92 <when input="format" value="6" format="strider" />
93 <when input="format" value="8" format="fasta" />
94 <when input="format" value="11" format="phylip" />
95 <when input="format" value="12" format="phylip" />
96 <when input="format" value="14" format="pir" />
97 <when input="format" value="17" format="nexus" />
98 <when input="format" value="18" format="prettyseq" />
99 <when input="format" value="19" format="xml" />
100 <when input="format" value="22" format="clustal" />
101 <when input="format" value="25" format="acedb" />
102 </change_format>
103 </data>
88 </outputs> 104 </outputs>
89 105
90 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> 106 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
91 <tests> 107 <tests>
92 <!-- [HELP] Test files have to be in the ~/test-data directory --> 108 <!-- [HELP] Test files have to be in the ~/test-data directory -->