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comparison genap2_kb_python/kb_count.xml @ 1:dbcb26e2a1db draft

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Updated tool version
author fwuennemann
date Mon, 19 Apr 2021 18:33:14 +0000
parents e8d93f1429c2
children 4da457a2c5dc
comparison
equal deleted inserted replaced
0:e8d93f1429c2 1:dbcb26e2a1db
1 <tool id="kb_python" name="kb_python" version="@VERSION@+galaxy0"> 1 <tool id="kb_python" name="kb_python" version="@VERSION@+galaxy1">
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>
7 <requirement type="package" version="0.25.1">kb-python</requirement>
8 </requirements>
9 <stdio> 6 <stdio>
10 <exit_code range="1:" /> 7 <exit_code range="1:" />
11 <exit_code range=":-1" /> 8 <exit_code range=":-1" />
12 <regex match="Error:" /> 9 <regex match="Error:" />
13 <regex match="Exception:" /> 10 <regex match="Exception:" />
53 #end if 50 #end if
54 -x $technology 51 -x $technology
55 #if $whitelist: 52 #if $whitelist:
56 --whitelist '${optional.whitelist}' 53 --whitelist '${optional.whitelist}'
57 #end if 54 #end if
58 #if $optional.multimap: 55 ${optional.multimap}
59 --mm 56 ${optional.report}
60 #end if
61 --workflow $workflow 57 --workflow $workflow
62 #if $extra_dtype != "none": 58 #if $extra_dtype != "none":
63 $extra_dtype 59 $extra_dtype
64 #end if 60 #end if
65 -o ./kb_outs 61 -o ./kb_outs
98 <option value="--h5ad">H5ad</option> 94 <option value="--h5ad">H5ad</option>
99 </param> 95 </param>
100 <section name="optional" title="Optional commands" expanded="false"> 96 <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 97 <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."/> 98 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?"/> 99 <param name="multimap" type="boolean" optional="true" truevalue="--mm" falsevalue="" label="Include multi pseudoaligned reads?" help="Do you want to include reads that pseudoalign to multiple genes?"/>
100 <param name="report" type="boolean" optional="true" truevalue="--report" falsevalue="" label="Create an html report?" help="If true, will create an html report with mapping statistics and cell" checked="false"/>
104 </section> 101 </section>
105 </inputs> 102 </inputs>
106 <outputs> 103 <outputs>
107 <data name="barcodes" label="cellranger barcodes" format="txt" from_work_dir="kb_outs/counts_unfiltered/cellranger/barcodes.tsv"/> 104 <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"/> 105 <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" /> 106 <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"/> 107 <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"/> 108 <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"/> 109 <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"/> 110 <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"/> 111 <filter>refTranscriptSource['TranscriptSource'] == "built"</filter>
112 </data>
113 <data name="t2g" label="t2g.txt" format="txt" from_work_dir="index/t2g.txt">
114 <filter>refTranscriptSource['TranscriptSource'] == "built"</filter>
115 </data>
115 <data name="cdna_t2c" label="-c1 cdna_t2c.txt" format="txt" from_work_dir="index/cdna_t2c.txt"> 116 <data name="cdna_t2c" label="-c1 cdna_t2c.txt" format="txt" from_work_dir="index/cdna_t2c.txt">
117 <filter>refTranscriptSource['TranscriptSource'] == "built"</filter>
116 <filter>workflow == "lamanno"</filter> 118 <filter>workflow == "lamanno"</filter>
117 </data> 119 </data>
118 <data name="intron_t2c" label="-c2 intron_t2c.txt" format="txt" from_work_dir="index/intron_t2c.txt"> 120 <data name="intron_t2c" label="-c2 intron_t2c.txt" format="txt" from_work_dir="index/intron_t2c.txt">
121 <filter>refTranscriptSource['TranscriptSource'] == "built"</filter>
119 <filter>workflow == "lamanno"</filter> 122 <filter>workflow == "lamanno"</filter>
120 </data> 123 </data>
121 <data name="adata" label="adata.h5ad" format="h5ad" from_work_dir="kb_outs/counts_unfiltered/adata.h5ad"> 124 <data name="adata" label="adata.h5ad" format="h5ad" from_work_dir="kb_outs/counts_unfiltered/adata.h5ad">
122 <filter >extra_dtype == "--h5ad"</filter> 125 <filter >extra_dtype == "--h5ad"</filter>
123 </data> 126 </data>
124 <data name="adata" label="adata.loom" format="loom" from_work_dir="kb_outs/counts_unfiltered/adata.loom"> 127 <data name="adata" label="adata.loom" format="loom" from_work_dir="kb_outs/counts_unfiltered/adata.loom">
125 <filter>extra_dtype == "--loom"</filter> 128 <filter>extra_dtype == "--loom"</filter>
129 </data>
130 <data name="report" label="report.html" format="html" from_work_dir="kb_outs/report.html">
131 <filter>optional["report"]</filter>
126 </data> 132 </data>
127 </outputs> 133 </outputs>
128 <tests> 134 <tests>
129 <expand macro="tests"/> 135 <expand macro="tests"/>
130 </tests> 136 </tests>