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comparison macros.xml @ 5:e572598580c2 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664"
author bgruening
date Sat, 25 Apr 2020 11:56:32 -0400
parents e53f19161c59
children 53d74155bb52
comparison
equal deleted inserted replaced
4:917f8e439160 5:e572598580c2
2 <token name="@VERSION@">0.14.1.2</token> 2 <token name="@VERSION@">0.14.1.2</token>
3 <token name="@GALAXY_VERSION@">galaxy0</token> 3 <token name="@GALAXY_VERSION@">galaxy0</token>
4 <token name="@IDX_VERSION@">q6</token> 4 <token name="@IDX_VERSION@">q6</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="1.0.6">bzip2</requirement> 7 <requirement type="package" version="1.3">seqtk</requirement>
8 <requirement type="package" version="1.2">seqtk</requirement>
9 <requirement type="package" version="0.14.1">salmon</requirement> 8 <requirement type="package" version="0.14.1">salmon</requirement>
10 <requirement type="package" version="1.9">samtools</requirement> 9 <requirement type="package" version="1.10">samtools</requirement>
11 <requirement type="package" version="0.2.0">vpolo</requirement> 10 <requirement type="package" version="0.2.0">vpolo</requirement>
12 <requirement type="package" version="1.17.2">numpy</requirement>
13 <requirement type="package" version="0.25.1">pandas</requirement> 11 <requirement type="package" version="0.25.1">pandas</requirement>
14 <requirement type="package" version="1.3.1">scipy</requirement> 12 <requirement type="package" version="1.3.1">scipy</requirement>
15 </requirements> 13 </requirements>
16 </xml> 14 </xml>
17 <xml name="stranded"> 15 <xml name="stranded">
284 <citations> 282 <citations>
285 <citation type="doi">10.1186/s13059-019-1670-y</citation> 283 <citation type="doi">10.1186/s13059-019-1670-y</citation>
286 <citation type="doi">10.1038/nmeth.4197</citation> 284 <citation type="doi">10.1038/nmeth.4197</citation>
287 </citations> 285 </citations>
288 </xml> 286 </xml>
287 <token name="@bam_sort@"><![CDATA[samtools sort -@ \${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam]]></token>
289 <token name="@indexing@"><![CDATA[ 288 <token name="@indexing@"><![CDATA[
290 mkdir ./index && 289 mkdir ./index &&
291 mkdir ./output && 290 mkdir ./output &&
292 #if $quant_type.refTranscriptSource.TranscriptSource != "indexed": 291 #if $quant_type.refTranscriptSource.TranscriptSource != "indexed":
293 salmon index -i ./index 292 salmon index -i ./index