Mercurial > repos > bgruening > salmon
comparison salmonquant.xml @ 13:e3d32471da11 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664"
| author | bgruening |
|---|---|
| date | Sat, 25 Apr 2020 11:49:15 -0400 |
| parents | 4de6e2e40c7a |
| children | 49121db48873 |
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| 12:7fdb9d1591e2 | 13:e3d32471da11 |
|---|---|
| 1 <tool id="salmon" name="Salmon quant" version="@VERSION@"> | 1 <tool id="salmon" name="Salmon quant" version="@VERSION@+galaxy1"> |
| 2 <description>Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads</description> | 2 <description>Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 10 @salreads@ | 10 @salreads@ |
| 11 #else: | 11 #else: |
| 12 @salalign@ | 12 @salalign@ |
| 13 #end if | 13 #end if |
| 14 @salquant@ | 14 @salquant@ |
| 15 #if $quant_type.qtype == "reads": | 15 #if $quant_type.qtype == "reads" and $quant_type.writeMappings: |
| 16 #if $quant_type.writeMappings: | 16 && @bam_sort@ ./output/samout.sam |
| 17 && samtools view -S -b ./output/samout.sam > ./output/bamout.bam | |
| 18 #end if | |
| 19 #end if | 17 #end if |
| 20 #if $quant_type.qtype == "alignment": | 18 #if $quant_type.qtype == "alignment" and $quant_type.sampleOut: |
| 21 #if $quant_type.sampleOut: | 19 && @bam_sort@ ./output/postSample.bam |
| 22 && samtools sort -@ 4 -o ./output/postSample_sorted.bam ./output/postSample.bam | |
| 23 #end if | |
| 24 #end if | 20 #end if |
| 25 ]]> | 21 ]]> |
| 26 </command> | 22 </command> |
| 27 <inputs> | 23 <inputs> |
| 28 <conditional name="quant_type"> | 24 <conditional name="quant_type"> |
| 46 <filter>geneMap</filter> | 42 <filter>geneMap</filter> |
| 47 </data> | 43 </data> |
| 48 <data name="output_bam" format="bam" from_work_dir="output/bamout.bam" label="${tool.name} on ${on_string} (BAM format)"> | 44 <data name="output_bam" format="bam" from_work_dir="output/bamout.bam" label="${tool.name} on ${on_string} (BAM format)"> |
| 49 <filter>quant_type['qtype'] == "reads" and quant_type['writeMappings']</filter> | 45 <filter>quant_type['qtype'] == "reads" and quant_type['writeMappings']</filter> |
| 50 </data> | 46 </data> |
| 51 <data name="postSample" format="bam" from_work_dir="./output/postSample_sorted.bam" label="Sampled input alignments on ${on_string}(BAM format)"> | 47 <data name="postSample" format="bam" from_work_dir="output/bamout.bam" label="Sampled input alignments on ${on_string}(BAM format)"> |
| 52 <filter>quant_type['qtype'] == "alignment" and quant_type['sampleOut']</filter> | 48 <filter>quant_type['qtype'] == "alignment" and quant_type['sampleOut']</filter> |
| 53 </data> | 49 </data> |
| 54 </outputs> | 50 </outputs> |
| 55 <tests> | 51 <tests> |
| 56 <test expect_num_outputs="2"> | 52 <test expect_num_outputs="2"> |