Mercurial > repos > bgruening > salmonquantmerge
comparison macros.xml @ 3:f6e3a10a88e5 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664"
| author | bgruening |
|---|---|
| date | Sat, 25 Apr 2020 11:52:56 -0400 |
| parents | 178ebdfe5a7e |
| children | 85b3dc9b6830 |
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| 2:178ebdfe5a7e | 3:f6e3a10a88e5 |
|---|---|
| 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 |