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comparison genap2_kb_python/kb_count.xml @ 0:e8d93f1429c2 draft

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author fwuennemann
date Fri, 16 Apr 2021 18:18:21 +0000
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1 <tool id="kb_python" name="kb_python" version="@VERSION@+galaxy0">
2 <description>performs gene and feature quantification on single-cell sequencing data.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="0.25.1">kb-python</requirement>
8 </requirements>
9 <stdio>
10 <exit_code range="1:" />
11 <exit_code range=":-1" />
12 <regex match="Error:" />
13 <regex match="Exception:" />
14 <regex match="Exception :" />
15 </stdio>
16 <command detect_errors="exit_code"><![CDATA[
17 mkdir ./index
18 && mkdir ./kb_outs
19 #if $refTranscriptSource.TranscriptSource == "history":
20 && ln -s '${refTranscriptSource.h_index.index_file}' './index/kb_ref.idx'
21 && ln -s '${refTranscriptSource.h_index.t2g_file}' './index/t2g.txt'
22 #if $workflow == "lamanno" or $workflow == "nucleus":
23 && ln -s '${refTranscriptSource.h_index.history_lamanno.cdna_t2c}' './index/cdna_t2c.txt'
24 && ln -s '${refTranscriptSource.h_index.history_lamanno.intron_t2c}' './index/intron_t2c.txt'
25 #end if
26 #set $index_path = './index'
27 #else if $refTranscriptSource.TranscriptSource == "built":
28 && kb ref -i ./index/kb_ref.idx
29 -g ./index/t2g.txt
30 -f1 ./index/cdna.fa
31 --workflow $workflow
32 #if $workflow == "lamanno" or $workflow == "nucleus":
33 -f2 ./index/intron.fa
34 -c1 ./index/cdna_t2c.txt
35 -c2 ./index/intron_t2c.txt
36 --workflow $workflow
37 #end if
38 #if $workflow != "kite":
39 '${refTranscriptSource.s_index.genomic_fasta}'
40 '${refTranscriptSource.s_index.genomic_gtf}'
41 #else:
42 '${refTranscriptSource.s_index.kite_table}'
43 #end if
44 #set $index_path = './index'
45 #end if
46 && kb count
47 -t \${GALAXY_SLOTS:-1}
48 -i $index_path/kb_ref.idx
49 -g $index_path/t2g.txt
50 #if $workflow == "lamanno" or $workflow == "nucleus":
51 -c1 $index_path/cdna_t2c.txt
52 -c2 $index_path/intron_t2c.txt
53 #end if
54 -x $technology
55 #if $whitelist:
56 --whitelist '${optional.whitelist}'
57 #end if
58 #if $optional.multimap:
59 --mm
60 #end if
61 --workflow $workflow
62 #if $extra_dtype != "none":
63 $extra_dtype
64 #end if
65 -o ./kb_outs
66 --cellranger
67 $FASTQ1
68 $FASTQ2
69 ]]>
70 </command>
71 <inputs>
72 <param name="workflow" label="Select the workflow you want to use:" type="select" multiple="false" format="text" help="Type of workflow. Use `lamanno` for RNA velocity based on La Manno et al. 2018 logic.
73 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 <option value="standard">standard</option>
75 <option value="lamanno">lamanno</option>
76 <option value="nucleus">nucleus</option>
77 <option value="kite">kite</option>
78 </param>
79 <expand macro="index"/>
80 <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.">
81 <option value="10XV1">10XV1</option>
82 <option value="10XV2">10XV2</option>
83 <option value="10XV3">10XV3</option>
84 <option value="CELSEQ">CELSEQ</option>
85 <option value="CELSEQ2">CELSEQ2</option>
86 <option value="DROPSEQ">DROPSEQ</option>
87 <option value="INDROPSV1">INDROPSV1</option>
88 <option value="INDROPSV2">INDROPSV2</option>
89 <option value="INDROPSV3">INDROPSV3</option>
90 <option value="SCRUBSEQ">SCRUBSEQ</option>
91 <option value="SURECELL">SURECELL</option>
92 </param>
93 <param name="FASTQ1" label="Select the R1 fastq file:" type="data" format="fastqsanger.gz" multiple="false"/>
94 <param name="FASTQ2" label="Select the R2 fastq file:" type="data" format="fastqsanger.gz" multiple="false"/>
95 <param name="extra_dtype" type="select" label="Do you want any additional output data type beside CellRanger?">
96 <option value="none" selected = "true">No</option>
97 <option value="--loom">Loom</option>
98 <option value="--h5ad">H5ad</option>
99 </param>
100 <section name="optional" title="Optional commands" expanded="false">
101 <param name="whitelist" type="data" format="tsv,tabular" optional="true" label="Whitelist file" help="Whitelisted barcodes to correct to. If not provided and bustools supports the technology, a pre-packaged whitelist is used. If not, the bustools
102 whitelist command is used."/>
103 <param name="multimap" type="boolean" optional="true" label="Include multi pseudoaligned reads?" help="Do you want to include reads that pseudoalign to multiple genes?"/>
104 </section>
105 </inputs>
106 <outputs>
107 <data name="barcodes" label="cellranger barcodes" format="txt" from_work_dir="kb_outs/counts_unfiltered/cellranger/barcodes.tsv"/>
108 <data name="genes" label="cellranger genes" format="txt" from_work_dir="kb_outs/counts_unfiltered/cellranger/genes.tsv"/>
109 <data name="matrix" label="cellranger matrix" format="mtx" from_work_dir="kb_outs/counts_unfiltered/cellranger/matrix.mtx" />
110 <data name="inspect" label="inspect_report" format="json" from_work_dir="kb_outs/inspect.json"/>
111 <data name="runinfo" label="run info" format="json" from_work_dir="kb_outs/run_info.json"/>
112 <data name="kbinfo" label="kb info" format="json" from_work_dir="kb_outs/kb_info.json"/>
113 <data name="kb_ref" label="kb_ref.idx" format="kallisto.idx" from_work_dir="index/kb_ref.idx"/>
114 <data name="t2g" label="t2g.txt" format="txt" from_work_dir="index/t2g.txt"/>
115 <data name="cdna_t2c" label="-c1 cdna_t2c.txt" format="txt" from_work_dir="index/cdna_t2c.txt">
116 <filter>workflow == "lamanno"</filter>
117 </data>
118 <data name="intron_t2c" label="-c2 intron_t2c.txt" format="txt" from_work_dir="index/intron_t2c.txt">
119 <filter>workflow == "lamanno"</filter>
120 </data>
121 <data name="adata" label="adata.h5ad" format="h5ad" from_work_dir="kb_outs/counts_unfiltered/adata.h5ad">
122 <filter >extra_dtype == "--h5ad"</filter>
123 </data>
124 <data name="adata" label="adata.loom" format="loom" from_work_dir="kb_outs/counts_unfiltered/adata.loom">
125 <filter>extra_dtype == "--loom"</filter>
126 </data>
127 </outputs>
128 <tests>
129 <expand macro="tests"/>
130 </tests>
131 <help><![CDATA[
132 This is a galaxy wrapper for kallisto-bustools (kb) for quantification of different types of single-cell sequencing data. The main kallisto-bustools homepage can be found under:
133 'kallisto-bustools<https://www.kallistobus.tools/>'.
134
135 The kb count command runs the kallisto and bustools programs. It can be used for pre-processing of data from a variety of single-cell RNA-seq technologies,
136 and for a number of different workflows (e.g. production of gene count matrices, RNA velocity analyses, etc.).
137
138 The kb package is developed and maintained by the Pachterlab under the MIT License.
139 ]]></help>
140 <citations>
141 <citation type="doi">https://doi.org/10.1101/673285</citation>
142 </citations>
143 </tool>