diff mircounts.xml @ 13:b045c30fb768 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"

--- a/mircounts.xml	Sat May 12 09:06:24 2018 -0400
+++ b/mircounts.xml	Fri Oct 18 19:18:50 2019 -0400
@@ -1,11 +1,11 @@
-<tool id="mircounts" name="miRcounts" version="1.3.2">
+<tool id="mircounts" name="miRcounts" version="1.4.0">
     <description> Counts miRNA alignments from small RNA sequence data</description>
     <requirements>
         <requirement type="package" version="1.2.0">bowtie</requirement>
-        <requirement type="package" version="1.6.0">samtools</requirement>
-        <requirement type="package" version="0.11.2.2">pysam</requirement>
-        <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
-        <requirement type="package" version="0.20_34=r3.3.2_0">r-lattice</requirement>
+        <requirement type="package" version="1.9=h10a08f8_12">samtools</requirement>
+        <requirement type="package" version="0.15.3=py27hda2845c_1">pysam</requirement>
+        <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement>
+        <requirement type="package" version="0.20_38=r36hcdcec82_1002">r-lattice</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" level="warning" description="Tool exception" />
@@ -31,7 +31,7 @@
             ln -f -s '$cutadapt.clipped_input' clipped_input.fastq &&
         #end if
         bowtie-build hairpin.fa hairpin &&
-        bowtie -v $v -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq | samtools sort -O bam -o '$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
         #if $plotting.plottingOption == 'yes':
@@ -135,6 +135,23 @@
     </outputs>
     <tests>
         <test>
+            <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="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"/>
+            <output name="gff3" file="aga.22.gff3" lines_diff="22"/>
+            <output name="pre_mir_count_file" file="aga_pre_mirs_count.22.tab"/>
+            <output name="mir_count_file" file="aga_mirs_count.22.tab"/>
+            <output name="latticePDF" file="aga_mir_coverage.pdf"/>
+            <output name="coverage_dataframe" file="aga_lattice_dataframe.tab"/>
+        </test>
+        <test>
             <param name="cutoption" value="yes" />
             <param name="min" value="18"/>
             <param name="max" value="32"/>