Mercurial > repos > scottx611x > qualimap2_bamqc

comparison qualimap_bamqc.xml @ 23:cefa83db3ebf draft

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planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
author scottx611x
date Thu, 26 Jul 2018 15:58:53 -0400
parents ffc7fdae906c
children 7e359370b5a2
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22:ffc7fdae906c 23:cefa83db3ebf
9 <exit_code range="1:" /> 9 <exit_code range="1:" />
10 </stdio> 10 </stdio>
11 <command interpreter="python"> 11 <command interpreter="python">
12 qualimap_bamqc.py 12 qualimap_bamqc.py
13 --input_file $input_realigned_bam_file 13 --input_file $input_realigned_bam_file
14 --out_dir qualimap_results
15 --out_genome_file $genome_coverage 14 --out_genome_file $genome_coverage
16 --java_mem_size $mem_size 15 --java_mem_size $mem_size
17 </command> 16 </command>
18 <inputs> 17 <inputs>
19 <param name="input_realigned_bam_file" type="data" format="bam" label="Realigned BAM dataset" help="Specify realigned BAM dataset"/> 18 <param name="input_realigned_bam_file" type="data" format="bam" label="Realigned BAM dataset" help="Specify realigned BAM dataset"/>
20 <param name="mem_size" type="text" value="8G" format="txt" label="Java memory size (default Gig)" help="Specify the size of memory to allocate. (Default 8 Gig)"/> 19 <param name="mem_size" type="text" value="8G" format="txt" label="Java memory size (default Gig)" help="Specify the size of memory to allocate. (Default 8 Gig)"/>
21 </inputs> 20 </inputs>
22 <outputs> 21 <outputs>
23 <data format="txt" name="genome_coverage" label="Qualimap BamQC Coverage Report"></data> 22 <data format="txt" name="genome_coverage" label="Qualimap BamQC Coverage Report for: ${on_string}"></data>
24 <data format="txt" name="genome_results" label="Qualimap BamQC Results"> 23 <data format="txt" name="genome_results" label="Qualimap BamQC Results for: ${on_string}"></data>
25 <discover_datasets pattern="genome_results.txt" visible="true" ext="txt" directory="qualimap_results" assign_primary_output="true"/> 24 <data format="html" name="qualimap_html_results" label="Qualimap BamQC HTML Report for: ${on_string}"></data>
26 </data> 25 <data format="zip" name="raw_data_qualimapReport" label="Qualimap Raw Data Results for: ${on_string}"></data>
27 <data format="html" name="qualimap_html_results" label="Qualimap BamQC HTML Report">
28 <discover_datasets pattern="qualimapReport.html" visible="true" ext="html" directory="qualimap_results" assign_primary_output="true"/>
29 </data>
30 <data format="txt" name="qualimap_raw_data_results" label="Qualimap Raw Data Results">
31 <discover_datasets pattern="__designation_and_ext__" visible="true" ext="txt" directory="qualimap_results/raw_data_qualimapReport"/>
32 </data>
33 </outputs> 26 </outputs>
34 27
35 <tests> 28 <tests>
36 <test> 29 <test>
37 <param name="mem_size" value="2G"></param> 30 <param name="mem_size" value="2G"></param>