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comparison pureclip.xml @ 2:0c87195035ee draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit c4a054d38cb9fe724612ba666f5a6d3e3ef49e75
author iuc
date Thu, 21 Jul 2022 19:17:16 +0000
parents 446f97577a12
children
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1:446f97577a12 2:0c87195035ee
1 <tool id="pureclip" name="PureCLIP" version="1.0.4"> 1 <tool id="pureclip" name="PureCLIP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.01">
2 <description>- HMM based peak caller designed for eCLIP/iCLIP data</description> 2 <description>- HMM based peak caller designed for eCLIP/iCLIP data</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.0.4</token>
5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros>
3 <requirements> 7 <requirements>
4 <requirement type="package" version="1.0.4">pureclip</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">pureclip</requirement>
5 </requirements> 9 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
7 ln -s '${target_bam_file}' target.bam && 11 ln -s '${target_bam_file}' target.bam &&
8 ln -f -s '${target_bam_file.metadata.bam_index}' target.bam.bai && 12 ln -f -s '${target_bam_file.metadata.bam_index}' target.bam.bai &&
9 ln -s '${genome_fasta_file}' genome.fa && 13 ln -s '${genome_fasta_file}' genome.fa &&
261 <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/> 265 <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>
262 <param name="motif_data_selector" value="supply_CL_motifs"/> 266 <param name="motif_data_selector" value="supply_CL_motifs"/>
263 <param name="cl_motif_bed_file" value="fimo_clmotif_occurences.chrM:4000-8300.bed" ftype="bed"/> 267 <param name="cl_motif_bed_file" value="fimo_clmotif_occurences.chrM:4000-8300.bed" ftype="bed"/>
264 <param name="max_motif_id" value="4"/> 268 <param name="max_motif_id" value="4"/>
265 <param name="crosslink_bed_stats" value="True"/> 269 <param name="crosslink_bed_stats" value="True"/>
266 <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed"/> 270 <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed" compare="re_match"/>
267 <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.cov_CLmotifs.bed"/> 271 <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.cov_CLmotifs.bed" compare="re_match"/>
268 <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats"/> 272 <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats" compare="re_match"/>
269 </test> 273 </test>
270 <test> 274 <test>
271 <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/> 275 <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
272 <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/> 276 <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>
273 <param name="control_bam_file" value="input.aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/> 277 <param name="control_bam_file" value="input.aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>