Mercurial > repos > fwuennemann > kb_python
comparison genap2_kb_python/kb_count.xml @ 3:1ecec9b9dde7 draft default tip
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| author | fwuennemann |
|---|---|
| date | Sat, 01 May 2021 16:20:44 +0000 |
| parents | 4da457a2c5dc |
| children |
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| 2:4da457a2c5dc | 3:1ecec9b9dde7 |
|---|---|
| 1 <tool id="kb_python" name="kb_python" version="@VERSION@+galaxy1"> | 1 <tool id="kb_python" name="kb_python" version="@VERSION@+galaxy2"> |
| 2 <description>performs gene and feature quantification on single-cell sequencing data.</description> | 2 <description>performs gene and feature quantification on single-cell sequencing data.</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <requirements> | 6 <requirements> |
| 35 -f2 ./index/intron.fa | 35 -f2 ./index/intron.fa |
| 36 -c1 ./index/cdna_t2c.txt | 36 -c1 ./index/cdna_t2c.txt |
| 37 -c2 ./index/intron_t2c.txt | 37 -c2 ./index/intron_t2c.txt |
| 38 --workflow $workflow | 38 --workflow $workflow |
| 39 #end if | 39 #end if |
| 40 #if $workflow != "kite": | 40 #if $workflow != "kite" and $workflow != "kite:10xFB": |
| 41 '${refTranscriptSource.s_index.genomic_fasta}' | 41 '${refTranscriptSource.s_index.genomic_fasta}' |
| 42 '${refTranscriptSource.s_index.genomic_gtf}' | 42 '${refTranscriptSource.s_index.genomic_gtf}' |
| 43 #else: | 43 #else: |
| 44 '${refTranscriptSource.s_index.kite_table}' | 44 '${refTranscriptSource.s_index.kite_table}' |
| 45 #end if | 45 #end if |
| 74 Use `nucleus` for RNA velocity on single-nucleus RNA-seq reads. Use `kite` for feature barcoding. Use `kite:10xFB` for 10x Genomics Feature Barcoding technology."> | 74 Use `nucleus` for RNA velocity on single-nucleus RNA-seq reads. Use `kite` for feature barcoding. Use `kite:10xFB` for 10x Genomics Feature Barcoding technology."> |
| 75 <option value="standard">standard</option> | 75 <option value="standard">standard</option> |
| 76 <option value="lamanno">lamanno</option> | 76 <option value="lamanno">lamanno</option> |
| 77 <option value="nucleus">nucleus</option> | 77 <option value="nucleus">nucleus</option> |
| 78 <option value="kite">kite</option> | 78 <option value="kite">kite</option> |
| 79 <option value="kite:10xFB">kite:10xFB (CITe-seq with Feature barcoding)</option> | |
| 79 </param> | 80 </param> |
| 80 <expand macro="index"/> | 81 <expand macro="index"/> |
| 81 <param name="technology" label="Select the scRNA-seq technology:" type="select" multiple="false" format="text" help="Choose the scRNA-seq technology used to generate the fastq data."> | 82 <param name="technology" label="Select the scRNA-seq technology:" type="select" multiple="false" format="text" help="Choose the scRNA-seq technology used to generate the fastq data."> |
| 82 <option value="10XV1">10XV1</option> | 83 <option value="10XV1">10XV1</option> |
| 83 <option value="10XV2">10XV2</option> | 84 <option value="10XV2">10XV2</option> |