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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
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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>