Mercurial > repos > bgruening > alevin
comparison alevin.xml @ 3:0a5258e41227 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit cf916eb507ee224812b64663c1d6020eb59eb88c"
| author | bgruening |
|---|---|
| date | Thu, 17 Oct 2019 17:05:18 -0400 |
| parents | e53f19161c59 |
| children | 917f8e439160 |
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| 2:e53f19161c59 | 3:0a5258e41227 |
|---|---|
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
| 8 mkdir ./index | 8 mkdir ./index |
| 9 && mkdir ./output | 9 && mkdir ./output |
| 10 #if '${refTranscriptSource.TranscriptSource}' != "indexed": | 10 #if $refTranscriptSource.TranscriptSource != "indexed": |
| 11 && salmon index -i ./index | 11 && salmon index -i ./index |
| 12 --kmerLen '${refTranscriptSource.s_index.kmer}' | 12 --kmerLen '${refTranscriptSource.s_index.kmer}' |
| 13 --gencode | 13 --gencode |
| 14 --transcripts '${refTranscriptSource.s_index.fasta}' | 14 --transcripts '${refTranscriptSource.s_index.fasta}' |
| 15 #set $index_path = './index' | 15 #set $index_path = './index' |
| 147 <param name="maxNumBarcodes" type="integer" optional="true" help="Maximum allowable limit to process the cell barcodes. Defaults to 100000"/> | 147 <param name="maxNumBarcodes" type="integer" optional="true" help="Maximum allowable limit to process the cell barcodes. Defaults to 100000"/> |
| 148 </section> | 148 </section> |
| 149 </inputs> | 149 </inputs> |
| 150 <outputs> | 150 <outputs> |
| 151 <data name="quants_mat.tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv"> | 151 <data name="quants_mat.tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv"> |
| 152 <filter>not optional["dumpMtx"]</filter> | 152 <filter>optional["dumpMtx"] is not True</filter> |
| 153 </data> | 153 </data> |
| 154 <data name="quants_mat.mtx.gz" label="quants_mat.mtx.gz" format="mtx" from_work_dir="output/alevin/quants_mat.mtx.gz"> | 154 <data name="quants_mat.mtx.gz" label="quants_mat.mtx.gz" format="mtx" from_work_dir="output/alevin/quants_mat.mtx.gz"> |
| 155 <filter>optional["dumpMtx"]</filter> | 155 <filter>optional["dumpMtx"]</filter> |
| 156 </data> | 156 </data> |
| 157 <data name="quants_mat_cols.txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/> | 157 <data name="quants_mat_cols.txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/> |