mircounts: mircounts.xml comparison

comparison mircounts.xml @ 15:ffcd42f85b61 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 5eb8570dce4e22fb2759cc16c8e1ce9d304508fe

author	artbio
date	Sat, 10 Feb 2024 17:15:04 +0000
parents	c163574c246f
children

comparison

equal deleted inserted replaced

-:c163574c246f
+:ffcd42f85b61
-<tool id="mircounts" name="miRcounts" version="1.5.1">
+<tool id="mircounts" name="miRcounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
 <description> Counts miRNA alignments from small RNA sequence data</description>
+<macros>
+<token name="@TOOL_VERSION@">1.6</token>
+<token name="@VERSION_SUFFIX@">0</token>
+<token name="@PROFILE@">23.0</token>
+</macros>
 <requirements>
-<requirement type="package" version="1.34=ha1f6473_0">tar</requirement>
+<requirement type="package" version="1.34">tar</requirement>
-<requirement type="package" version="1.3.0=py39h176da8b_2">bowtie</requirement>
+<requirement type="package" version="1.3.1">bowtie</requirement>
-<requirement type="package" version="1.12=h9aed4be_1">samtools</requirement>
+<requirement type="package" version="1.19.2">samtools</requirement>
-<requirement type="package" version="0.16.0.1=py39h051187c_3">pysam</requirement>
+<requirement type="package" version="0.22.0">pysam</requirement>
-<requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement>
+<requirement type="package" version="1.7.4">r-optparse</requirement>
-<requirement type="package" version="0.20_44=r40hcfec24a_0">r-lattice</requirement>
+<requirement type="package" version="0.22_5">r-lattice</requirement>
 </requirements>
 <stdio>
 <exit_code range="1:" level="warning" description="Tool exception" />
 </stdio>
 <command detect_errors="exit_code"><![CDATA[
 tar -xf  '$__tool_directory__'/mirbase.tar.gz &&
 python '$__tool_directory__'/mature_mir_gff_translation.py
---gff_path mirbase/${mirbase_version}/genomes/${genomeKey}.gff3
+--gff_path mirbase/'${mirbase_version}'/genomes/'${genomeKey}'.gff3
---output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript".
+--output '$gff3' && ## transcode mature miR genome coordinates relative to "miRNA_primary_transcript"
 python '$__tool_directory__'/format_fasta_hairpins.py
---hairpins_path mirbase/${mirbase_version}/hairpin.fa.gz
+--hairpins_path mirbase/'${mirbase_version}'/hairpin.fa.gz
---basename ${genomeKey}
+--basename '${genomeKey}'
 --output hairpin.fa &&
 #if $cutadapt.cutoption == "yes":
-python '$__tool_directory__'/yac.py --input $cutadapt.input
+python '$__tool_directory__'/yac.py --input '$cutadapt.input'
 --output clipped_input.fastq
 --output_format fastq
---adapter_to_clip $cutadapt.clip_source.clip_sequence
+--adapter_to_clip '$cutadapt.clip_source.clip_sequence'
---min $cutadapt.min
+--min '$cutadapt.min'
---max $cutadapt.max
+--max '$cutadapt.max'
---Nmode $cutadapt.Nmode &&
+--Nmode '$cutadapt.Nmode' &&
 #else:
 ln -f -s '$cutadapt.clipped_input' clipped_input.fastq &&
 #end if
 bowtie-build hairpin.fa hairpin &&
-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' &&
+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' &&
 samtools index $output &&
-python '$__tool_directory__'/mircounts.py --alignment $output --gff $gff3 --quality_threshold 10 --pre_mirs $pre_mir_count_file --mirs $mir_count_file --lattice $coverage_dataframe
+python '$__tool_directory__'/mircounts.py --alignment '$output' --gff '$gff3' --quality_threshold 10 --pre_mirs '$pre_mir_count_file' --mirs '$mir_count_file' --lattice '$coverage_dataframe'
 #if $plotting.plottingOption == 'yes':
-&& Rscript '$__tool_directory__'/coverage_plotting.R --dataframe $coverage_dataframe --type $plotting.display --output $latticePDF
+&& Rscript '$__tool_directory__'/coverage_plotting.R --dataframe '$coverage_dataframe' --type '$plotting.display' --output '$latticePDF'
 #end if
 ]]></command>
 <inputs>
 <conditional name="cutadapt">
 <param label="Remove adapter sequence before aligning" name="cutoption" type="select">
 <data format="pdf" label="Pre-mir coverage (${plotting.display})" name="latticePDF">
 <filter>plotting['plottingOption'] == "yes"</filter>
 </data>
 </outputs>
 <tests>
-<test>
+<test expect_num_outputs="6">
-<param name="cutoption" value="no" />
+<param name="cutoption" value="no"/>
 <param name="v" value="1"/>
 <param name="genomeKey" value="aga"/>
 <param name="mirbase_version" value="22"/>
-<param name="clipped_input" value="aga.fastqsanger" ftype="fastqsanger"/>
+<param name="clipped_input" value="aga.fastqsanger.gz" ftype="fastqsanger.gz"/>
 <param name="plottingOption" value="yes"/>
 <param name="display" value="relative"/>
 <param name="output_premir_counts" value="True"/>
 <param name="output_mir_counts" value="True"/>
 <output name="output" file="aga.bam" compare="sim_size" />
 <output name="pre_mir_count_file" file="aga_pre_mirs_count.22.tab" ftype="tabular" />
 <output name="mir_count_file" file="aga_mirs_count.22.tab" ftype="tabular" />
 <output name="latticePDF" file="aga_mir_coverage.pdf" ftype="pdf" />
 <output name="coverage_dataframe" file="aga_lattice_dataframe.tab" ftype="tabular" />
 </test>
-<test>
+<test expect_num_outputs="6">
-<param name="cutoption" value="yes" />
+<param name="cutoption" value="yes"/>
 <param name="min" value="18"/>
 <param name="max" value="32"/>
 <param name="Nmode" value="reject"/>
 <param name="clip_sequence" value="TGGAATTCTCGGGTGCCAAG"/>
 <param name="v" value="1"/>
 <output name="pre_mir_count_file" file="mouse_pre_mirs_count.29.tab" ftype="tabular" />
 <output name="mir_count_file" file="mouse_mirs_count.29.tab" ftype="tabular" />
 <output name="latticePDF" file="mouse_mir_coverage.pdf" ftype="pdf" />
 <output name="coverage_dataframe" file="mouse_lattice_dataframe.tab" ftype="tabular" />
 </test>
-<test>
+<test expect_num_outputs="4">
-<param name="cutoption" value="yes" />
+<param name="cutoption" value="yes"/>
 <param name="min" value="15"/>
 <param name="max" value="25"/>
 <param name="Nmode" value="reject"/>
 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
 <param name="v" value="0"/>
 <output name="output" file="unclipped.out.22.bam" compare="sim_size" />
 <output name="gff3" file="translated_dme.22.gff3" lines_diff="22" ftype="gff3" />
 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.22.tab" ftype="tabular" />
 <output name="mir_count_file" file="mirs_unclipped_count.22.tab" ftype="tabular" />
 </test>
-<test>
+<test expect_num_outputs="4">
-<param name="cutoption" value="yes" />
+<param name="cutoption" value="yes"/>
 <param name="min" value="15"/>
 <param name="max" value="25"/>
 <param name="Nmode" value="reject"/>
 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
 <param name="v" value="0"/>
 <output name="output" file="unclipped.out.bam" compare="sim_size" />
 <output name="gff3" file="translated_dme.gff3" lines_diff="22"  ftype="gff3" />
 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab" ftype="tabular" />
 <output name="mir_count_file" file="mirs_unclipped_count.tab" ftype="tabular" />
 </test>
-<test>
+<test expect_num_outputs="6">
-<param name="cutoption" value="yes" />
+<param name="cutoption" value="yes"/>
 <param name="min" value="15"/>
 <param name="max" value="25"/>
 <param name="Nmode" value="reject"/>
 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
 <param name="v" value="0"/>
 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab" ftype="tabular" />
 <output name="mir_count_file" file="mirs_unclipped_count.tab" ftype="tabular" />
 <output name="latticePDF" file="mir_unclipped_coverage.pdf" ftype="pdf"/>
 <output name="coverage_dataframe" file="lattice_unclipped_dataframe.tab" ftype="tabular" />
 </test>
-<test>
+<test expect_num_outputs="6">
-<param name="cutoption" value="no" />
+<param name="cutoption" value="no"/>
 <param name="v" value="1"/>
 <param name="genomeKey" value="dme"/>
 <param name="mirbase_version" value="21"/>
 <param name="clipped_input" value="input.clipped.fastqsanger" ftype="fastqsanger"/>
 <param name="plottingOption" value="yes"/>
 + Computes pre-mir and mir counts using the pysam python package
 + Plots pre-mir read coverages using R lattice package (optional)
 This tool uses a species-specific GFF3 file generated from mirBase_ to guide the parsing of a bam file of small RNA alignments.
-.. _mirBase: ftp://mirbase.org/pub/mirbase/
+.. _mirBase: https://mirbase.org/download/
 ------
 **Inputs**

Mercurial > repos > artbio > mircounts

comparison mircounts.xml @ 15:ffcd42f85b61 draft default tip