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comparison scpipe.xml @ 4:5660e3ea8795 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit c2ca988fbdfb512e79e78afb941e1e78de8294d7"
author iuc
date Fri, 16 Oct 2020 14:38:08 +0000
parents 9f8ce2980849
children 2a7c718bda2a
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3:25e52048c7cc 4:5660e3ea8795
1 <tool id="scpipe" name="scPipe" version="1.0.0+galaxy1"> 1 <tool id="scpipe" name="scPipe" version="1.0.0+galaxy2" profile="19.01">
2 <description>- preprocessing pipeline for single cell RNA-seq</description> 2 <description>- preprocessing pipeline for single cell RNA-seq</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.0">bioconductor-scpipe</requirement> 4 <requirement type="package" version="1.0.0">bioconductor-scpipe</requirement>
5 <requirement type="package" version="1.28.1">bioconductor-rsubread</requirement> 5 <requirement type="package" version="1.28.1">bioconductor-rsubread</requirement>
6 <!-- rhtslib can be removed with a newer scpipe package --> 6 <!-- rhtslib can be removed with a newer scpipe package -->
72 #end if 72 #end if
73 73
74 TAB=\$(printf '\t') && 74 TAB=\$(printf '\t') &&
75 75
76 #if $samples.barcodes: 76 #if $samples.barcodes:
77 sed -i.bak -e "s/\${TAB}/,/g" '$samples.barcodes' && 77 sed -e "s/\${TAB}/,/g" '$samples.barcodes' > samples.barcodes &&
78 #end if 78 #end if
79 79
80 ## Run scPipe 80 ## Run scPipe
81 81
82 Rscript '$__tool_directory__/scpipe.R' 82 Rscript '$__tool_directory__/scpipe.R'
83 83
84 #if $samples.format_select == "bam": 84 #if $samples.format_select == "bam":
85 --bam '$bam_name' 85 --bam '$bam_name'
86 --samplename '$bam_name' 86 --samplename '$bam_name'
87 --barcodes '$samples.barcodes' 87 --barcodes 'samples.barcodes'
88 #else: 88 #else:
89 --fasta '$fasta_name' 89 --fasta '$fasta_name'
90 --read1 '$in1_name' 90 --read1 '$in1_name'
91 --read2 '$in2_name' 91 --read2 '$in2_name'
92 --samplename '$in1_name' 92 --samplename '$in1_name'
93 #if $barcodes: 93 #if $samples.barcodes:
94 --barcodes '$samples.barcodes' 94 --barcodes 'samples.barcodes'
95 #end if 95 #end if
96 #end if 96 #end if
97 97
98 --exons '$anno_name' 98 --exons '$anno_name'
99 --organism '$organism' 99 --organism '$organism'
242 <tests> 242 <tests>
243 <!-- Ensure outputs work --> 243 <!-- Ensure outputs work -->
244 <test> 244 <test>
245 <param name="format_select" value="fastq" /> 245 <param name="format_select" value="fastq" />
246 <param name="fasta_source" value="history"/> 246 <param name="fasta_source" value="history"/>
247 <param name="ref_fa_hist" ftype="fasta" value="mm10_MT19.fa.gz"/> 247 <param name="ref_fa_hist" ftype="fasta.gz" value="mm10_MT19.fa.gz"/>
248 <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/> 248 <param name="exons" ftype="gff3.gz" value="mm10_MT19.gff3.gz"/>
249 <param name="organism" value="mmusculus_gene_ensembl"/> 249 <param name="organism" value="mmusculus_gene_ensembl"/>
250 <param name="paired_format_selector" value="paired" /> 250 <param name="paired_format_selector" value="paired" />
251 <param name="in1" ftype="fastqsanger.gz" value="CB51_MT19_R1.gz"/> 251 <param name="in1" ftype="fastqsanger.gz" value="CB51_MT19_R1.gz"/>
252 <param name="in2" ftype="fastqsanger.gz" value="CB51_MT19_R2.gz"/> 252 <param name="in2" ftype="fastqsanger.gz" value="CB51_MT19_R2.gz"/>
253 <param name="us" value="-1"/> 253 <param name="us" value="-1"/>
267 </test> 267 </test>
268 <!-- Ensure built-in fasta works --> 268 <!-- Ensure built-in fasta works -->
269 <test> 269 <test>
270 <param name="format_select" value="fastq" /> 270 <param name="format_select" value="fastq" />
271 <param name="fasta_source" value="cached"/> 271 <param name="fasta_source" value="cached"/>
272 <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/> 272 <param name="exons" ftype="gff3.gz" value="mm10_MT19.gff3.gz"/>
273 <param name="organism" value="mmusculus_gene_ensembl"/> 273 <param name="organism" value="mmusculus_gene_ensembl"/>
274 <param name="paired_format_selector" value="paired" /> 274 <param name="paired_format_selector" value="paired" />
275 <param name="in1" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R1.gz"/> 275 <param name="in1" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R1.gz"/>
276 <param name="in2" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R2.gz"/> 276 <param name="in2" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R2.gz"/>
277 <param name="us" value="-1"/> 277 <param name="us" value="-1"/>
286 <!-- Ensure BAM input works --> 286 <!-- Ensure BAM input works -->
287 <test> 287 <test>
288 <param name="format_select" value="bam" /> 288 <param name="format_select" value="bam" />
289 <param name="bam" ftype="bam" value="aligned.mapped.bam"/> 289 <param name="bam" ftype="bam" value="aligned.mapped.bam"/>
290 <param name="barcodes" ftype="tabular" value="barcode_anno.tsv"/> 290 <param name="barcodes" ftype="tabular" value="barcode_anno.tsv"/>
291 <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/> 291 <param name="exons" ftype="gff3.gz" value="mm10_MT19.gff3.gz"/>
292 <param name="organism" value="mmusculus_gene_ensembl"/> 292 <param name="organism" value="mmusculus_gene_ensembl"/>
293 <param name="us" value="-1"/> 293 <param name="us" value="-1"/>
294 <output name="out_matrix" > 294 <output name="out_matrix" >
295 <assert_contents> 295 <assert_contents>
296 <has_text text="ENSMUSG00000064351" /> 296 <has_text text="ENSMUSG00000064351" />
300 <!-- Ensure BAM input with QC outputs works --> 300 <!-- Ensure BAM input with QC outputs works -->
301 <test> 301 <test>
302 <param name="format_select" value="bam" /> 302 <param name="format_select" value="bam" />
303 <param name="bam" ftype="bam" value="aligned.mapped.bam"/> 303 <param name="bam" ftype="bam" value="aligned.mapped.bam"/>
304 <param name="barcodes" ftype="tabular" value="barcode_anno.tsv"/> 304 <param name="barcodes" ftype="tabular" value="barcode_anno.tsv"/>
305 <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/> 305 <param name="exons" ftype="gff3.gz" value="mm10_MT19.gff3.gz"/>
306 <param name="organism" value="mmusculus_gene_ensembl"/> 306 <param name="organism" value="mmusculus_gene_ensembl"/>
307 <param name="us" value="-1"/> 307 <param name="us" value="-1"/>
308 <param name="plots" value="True"/> 308 <param name="plots" value="True"/>
309 <param name="metrics_matrix" value="True"/> 309 <param name="metrics_matrix" value="True"/>
310 <output name="out_matrix" > 310 <output name="out_matrix" >