Mercurial > repos > iuc > multiqc
changeset 23:abfd8a6544d7 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
| author | iuc |
|---|---|
| date | Sat, 10 Dec 2022 11:22:18 +0000 |
| parents | 9a913cdee30e |
| children | |
| files | macros.xml multiqc.xml test-data/junction_annotation.txt test-data/junction_saturation.txt |
| diffstat | 4 files changed, 84 insertions(+), 22 deletions(-) [+] |
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--- a/macros.xml Wed Nov 03 15:17:39 2021 +0000 +++ b/macros.xml Sat Dec 10 11:22:18 2022 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.11</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">multiqc</xref> @@ -218,9 +218,11 @@ #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.GC.xls') ln -s '$file' '$file_path' && #end for - #elif str($repeat2.type.type) == "junction_annotation" - #set $pattern = "Group Total_bases Tag_count Tags/Kb" - @LN_3_FILES@ + #elif str($repeat2.type.type) == "junction_saturation" + #for $k, $file in enumerate($repeat2.type.input) + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.junctionSaturation_plot.r') + ln -s '${file}' '$file_path' && + #end for #elif str($repeat2.type.type) == "read_distribution" #set $pattern = "Group Total_bases Tag_count Tags/Kb" @LN_3_FILES@
--- a/multiqc.xml Wed Nov 03 15:17:39 2021 +0000 +++ b/multiqc.xml Sat Dec 10 11:22:18 2022 +0000 @@ -413,42 +413,42 @@ <repeat name="output" title="RSeQC output" min="1"> <conditional name="type"> <param name="type" type="select" label="Type of RSeQC output?"> - <option value="bam_stat">bam_stat</option> - <option value="gene_body_coverage">gene_body_coverage</option> - <option value="infer_experiment">infer_experiment</option> - <option value="inner_distance">inner_distance</option> - <option value="junction_annotation">junction_annotation</option> - <option value="junction_saturation">junction_saturation</option> - <option value="read_distribution">read_distribution</option> - <option value="read_duplication_pos">read_duplication_pos</option> - <option value="read_gc">read_gc</option> + <option value="bam_stat">BAM/SAM mapping stats</option> + <option value="gene_body_coverage">Gene body coverage</option> + <option value="infer_experiment">Infer experiment</option> + <option value="inner_distance">Inner distance</option> + <option value="junction_annotation">Junction annotation</option> + <option value="junction_saturation">Junction saturation</option> + <option value="read_distribution">Read distribution</option> + <option value="read_duplication_pos">Read duplication</option> + <option value="read_gc">Read GC</option> </param> <when value="bam_stat"> - <param name="input" type="data" format="txt,tabular" multiple="true" label="RSeQC bam_stat output" help="It should contain 'Proper-paired reads map to different chrom:'"/> + <param name="input" type="data" format="txt,tabular" multiple="true" label="RSeQC BAM stat: output file" help="It should contain 'Proper-paired reads map to different chrom:'"/> </when> <when value="gene_body_coverage"> - <param name="input" type="data" format="txt" multiple="true" label="RSeQC gene_body_coverage output"/> + <param name="input" type="data" format="txt" multiple="true" label="RSeQC gene body coverage: stats file"/> </when> <when value="infer_experiment"> - <param name="input" type="data" format="txt" multiple="true" label="RSeQC infer_experiment output" help="It should contain 'Fraction of reads explained by'"/> + <param name="input" type="data" format="txt" multiple="true" label="RSeQC infer experiment: configuration output" help="It should contain 'Fraction of reads explained by'"/> </when> <when value="inner_distance"> - <param name="input" type="data" format="txt,xls,tabular" multiple="true" label="RSeQC inner_distance output"/> + <param name="input" type="data" format="txt" multiple="true" label="RSeQC inner distance: frequency file"/> </when> <when value="junction_annotation"> - <param name="input" type="data" format="txt,xls,tabular" multiple="true" label="RSeQC junction_annotation output" help="It should contain 'Partial Novel Splicing Junctions:'"/> + <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction annotation: stats file" help="It should contain 'Partial Novel Splicing Junctions:'"/> </when> <when value="junction_saturation"> - <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction_saturation output"/> + <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction saturation: junction saturation plot Rscript file"/> </when> <when value="read_distribution"> - <param name="input" type="data" format="txt,xls,tabular" multiple="true" label="RSeQC read_distribution output" help="It should contain 'Group Total_bases Tag_count Tags/Kb'"/> + <param name="input" type="data" format="txt" multiple="true" label="RSeQC read distribution: stats output" help="It should contain 'Group Total_bases Tag_count Tags/Kb'"/> </when> <when value="read_duplication_pos"> - <param name="input" type="data" format="csv,xls,tabular" multiple="true" label="RSeQC read_duplication_pos output"/> + <param name="input" type="data" format="xls" multiple="true" label="RSeQC read duplication: positions XLS file"/> </when> <when value="read_gc"> - <param name="input" type="data" format="csv,xls,tabular" multiple="true" label="RSeQC read_gc output"/> + <param name="input" type="data" format="csv,xls,tabular" multiple="true" label="RSeQC read GC output"/> </when> </conditional> </repeat> @@ -1076,6 +1076,36 @@ </output> <output_collection name="stats" type="list" count="2"/> </test> + <!--Test 07--> + <test expect_num_outputs="2"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="rseqc" /> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="junction_annotation"/> + <param name="input" value="junction_annotation.txt"/> + </conditional> + </repeat> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="junction_saturation"/> + <param name="input" value="junction_saturation.txt"/> + </conditional> + </repeat> + </conditional> + </repeat> + <param name="title" value="RSEQC report"/> + <!-- <param name="flat" value="true"/> --> + <output name="html_report"> + <assert_contents> + <has_text text="RSEQC report" /> + <has_text text="Junction Annotation" /> + <has_text text="Junction Saturation" /> + </assert_contents> + </output> + <output_collection name="stats" type="list" count="2"/> + </test> </tests> <help><![CDATA[ **What it does**
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/junction_annotation.txt Sat Dec 10 11:22:18 2022 +0000 @@ -0,0 +1,18 @@ +Reading reference bed file: /tmp/tmpwdbqfb2i/files/000/dataset_3.dat ... Done +Load BAM file ... Done + +=================================================================== +Total splicing Events: 4 +Known Splicing Events: 1 +Partial Novel Splicing Events: 1 +Novel Splicing Events: 1 +Filtered Splicing Events: 1 + +Total splicing Junctions: 3 +Known Splicing Junctions: 1 +Partial Novel Splicing Junctions: 1 +Novel Splicing Junctions: 1 + +=================================================================== +Create BED file ... +Create Interact file ...
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/junction_saturation.txt Sat Dec 10 11:22:18 2022 +0000 @@ -0,0 +1,12 @@ +pdf('output.junctionSaturation_plot.pdf') +x=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100) +y=c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1) +z=c(0,0,0,0,0,0,1,1,1,1,1,1,1,2,2,2,2,2,2,3) +w=c(0,0,0,0,0,0,1,1,1,1,1,1,1,2,2,2,2,2,2,2) +m=max(0,0,0) +n=min(0,0,0) +plot(x,z/1000,xlab='percent of total reads',ylab='Number of splicing junctions (x1000)',type='o',col='blue',ylim=c(n,m)) +points(x,y/1000,type='o',col='red') +points(x,w/1000,type='o',col='green') +legend(5,0, legend=c("All junctions","known junctions", "novel junctions"),col=c("blue","red","green"),lwd=1,pch=1) +dev.off()