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comparison mircounts.xml @ 13:b045c30fb768 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
author artbio
date Fri, 18 Oct 2019 19:18:50 -0400
parents 6d3e98cba73a
children c163574c246f
comparison
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12:6d3e98cba73a 13:b045c30fb768
1 <tool id="mircounts" name="miRcounts" version="1.3.2"> 1 <tool id="mircounts" name="miRcounts" version="1.4.0">
2 <description> Counts miRNA alignments from small RNA sequence data</description> 2 <description> Counts miRNA alignments from small RNA sequence data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2.0">bowtie</requirement> 4 <requirement type="package" version="1.2.0">bowtie</requirement>
5 <requirement type="package" version="1.6.0">samtools</requirement> 5 <requirement type="package" version="1.9=h10a08f8_12">samtools</requirement>
6 <requirement type="package" version="0.11.2.2">pysam</requirement> 6 <requirement type="package" version="0.15.3=py27hda2845c_1">pysam</requirement>
7 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> 7 <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement>
8 <requirement type="package" version="0.20_34=r3.3.2_0">r-lattice</requirement> 8 <requirement type="package" version="0.20_38=r36hcdcec82_1002">r-lattice</requirement>
9 </requirements> 9 </requirements>
10 <stdio> 10 <stdio>
11 <exit_code range="1:" level="warning" description="Tool exception" /> 11 <exit_code range="1:" level="warning" description="Tool exception" />
12 </stdio> 12 </stdio>
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
29 --Nmode $cutadapt.Nmode && 29 --Nmode $cutadapt.Nmode &&
30 #else: 30 #else:
31 ln -f -s '$cutadapt.clipped_input' clipped_input.fastq && 31 ln -f -s '$cutadapt.clipped_input' clipped_input.fastq &&
32 #end if 32 #end if
33 bowtie-build hairpin.fa hairpin && 33 bowtie-build hairpin.fa hairpin &&
34 bowtie -v $v -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq | samtools sort -O bam -o '$output' && 34 bowtie -v $v -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o '$output' &&
35 samtools index $output && 35 samtools index $output &&
36 python '$__tool_directory__'/mircounts.py --alignment $output --gff $gff3 --quality_threshold 10 --pre_mirs $pre_mir_count_file --mirs $mir_count_file --lattice $coverage_dataframe 36 python '$__tool_directory__'/mircounts.py --alignment $output --gff $gff3 --quality_threshold 10 --pre_mirs $pre_mir_count_file --mirs $mir_count_file --lattice $coverage_dataframe
37 #if $plotting.plottingOption == 'yes': 37 #if $plotting.plottingOption == 'yes':
38 && Rscript '$__tool_directory__'/coverage_plotting.R --dataframe $coverage_dataframe --type $plotting.display --output $latticePDF 38 && Rscript '$__tool_directory__'/coverage_plotting.R --dataframe $coverage_dataframe --type $plotting.display --output $latticePDF
39 #end if 39 #end if
133 <filter>plotting['plottingOption'] == "yes"</filter> 133 <filter>plotting['plottingOption'] == "yes"</filter>
134 </data> 134 </data>
135 </outputs> 135 </outputs>
136 <tests> 136 <tests>
137 <test> 137 <test>
138 <param name="cutoption" value="no" />
139 <param name="v" value="1"/>
140 <param name="genomeKey" value="aga"/>
141 <param name="mirbase_version" value="22"/>
142 <param name="clipped_input" value="aga.fastqsanger" ftype="fastqsanger"/>
143 <param name="plottingOption" value="yes"/>
144 <param name="display" value="relative"/>
145 <param name="output_premir_counts" value="True"/>
146 <param name="output_mir_counts" value="True"/>
147 <output name="output" file="aga.bam"/>
148 <output name="gff3" file="aga.22.gff3" lines_diff="22"/>
149 <output name="pre_mir_count_file" file="aga_pre_mirs_count.22.tab"/>
150 <output name="mir_count_file" file="aga_mirs_count.22.tab"/>
151 <output name="latticePDF" file="aga_mir_coverage.pdf"/>
152 <output name="coverage_dataframe" file="aga_lattice_dataframe.tab"/>
153 </test>
154 <test>
138 <param name="cutoption" value="yes" /> 155 <param name="cutoption" value="yes" />
139 <param name="min" value="18"/> 156 <param name="min" value="18"/>
140 <param name="max" value="32"/> 157 <param name="max" value="32"/>
141 <param name="Nmode" value="reject"/> 158 <param name="Nmode" value="reject"/>
142 <param name="clip_sequence" value="TGGAATTCTCGGGTGCCAAG"/> 159 <param name="clip_sequence" value="TGGAATTCTCGGGTGCCAAG"/>