Mercurial > repos > scottx611x > qualimap2_bamqc

annotate qualimap_bamqc.xml @ 19:f2cac72e0eb1 draft

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planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
author scottx611x
date Thu, 26 Jul 2018 13:51:46 -0400
parents a6a7a1dd1e53
children d4d49c617455
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1 <?xml version="1.0" encoding="utf-8" ?>
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2 <tool id="qualimap_bamqc" name="QualiMap BamQC" version="2.2">
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3 <description>Tool to to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.</description>
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4 <requirements>
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5 <requirement type="package" version="2.2">qualimap</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range=":-1" />
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9 <exit_code range="1:" />
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10 </stdio>
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11 <command interpreter="python">
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12 qualimap_bamqc.py
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13 --input_file $input_realigned_bam_file
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14 --out_dir qualimap_results
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15 --out_genome_file $genome_coverage
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16 --java_mem_size $mem_size
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17 </command>
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18 <inputs>
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19 <param name="input_realigned_bam_file" type="data" format="bam" label="Realigned BAM dataset" help="Specify realigned BAM dataset"/>
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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)"/>
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21 </inputs>
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22 <outputs>
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23 <data format="txt" name="genome_coverage" label="Qualimap BamQC Coverage Report">
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24 <discover_datasets visible="true" ext="txt" assign_primary_output="true"/>
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25 </data>
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26 <data format="txt" name="genome_results" label="Qualimap BamQC Results">
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27 <discover_datasets pattern="genome_results.txt" visible="true" ext="txt" directory="qualimap_results" assign_primary_output="true"/>
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28 </data>
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29 <data format="html" name="qualimap_html_results" label="Qualimap BamQC HTML Report">
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30 <discover_datasets pattern="qualimapReport.html" visible="true" ext="html" directory="qualimap_results" assign_primary_output="true"/>
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31 </data>
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32 <data format="txt" name="qualimap_raw_data_results" label="Qualimap Raw Data Results">
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33 <discover_datasets visible="true" ext="txt" directory="qualimap_results" assign_primary_output="true"/>
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34 </data>
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35 </outputs>
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36
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37 <tests>
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38 <test>
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39 <param name="input_realigned_bam_file" value="test.bam"></param>
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40 <output name="genome_coverage">
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41 <assert_contents>
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42 <has_text text="" />
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43 </assert_contents>
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44 </output>
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45 <output name="genome_results">
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46 <assert_contents>
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47 <has_text text="" />
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48 </assert_contents>
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49 </output>
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50 <output name="qualimap_html_results">
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51 <assert_contents>
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52 <has_text text="" />
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53 </assert_contents>
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54 </output>
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55 </test>
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56 </tests>
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57 <help>
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58 https://github.com/scottx611x/qualimap2
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59 </help>
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60 <citations>
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61 </citations>
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62 </tool>