Mercurial > repos > fwuennemann > kb_python
comparison genap2_kb_python/kb_count.xml @ 1:dbcb26e2a1db draft
Updated tool version
author | fwuennemann |
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date | Mon, 19 Apr 2021 18:33:14 +0000 |
parents | e8d93f1429c2 |
children | 4da457a2c5dc |
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0:e8d93f1429c2 | 1:dbcb26e2a1db |
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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> |