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annotate callntvar.xml @ 9:18aad692772a draft default tip

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planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
author nml
date Mon, 20 Jun 2022 20:06:36 +0000
parents 9def47f3c1e4
children
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18aad692772a planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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1 <tool id="callntvar" name="Nucleotide Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>Identifies nucleotide variants</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
18aad692772a planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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18aad692772a planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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9 ln -s $input_bam '${input_bam.name}' &&
18aad692772a planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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10 ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
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18aad692772a planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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12 quasitools call ntvar '${input_bam.name}' $ref_file
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14 #if $error_rate:
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15 -e $error_rate
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16 #end if
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18 -o output.vcf
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20 ]]></command>
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21 <inputs>
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22 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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23 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
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24 <param name="error_rate" type="float" optional="true" min="0" max="1" value="0.0021" label="Error rate" help="Estimated sequencing error rate. Defaults to 0.0021."/>
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25 </inputs>
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26 <outputs>
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27 <data format="vcf" name="output" from_work_dir="output.vcf" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input_bam" value="align.bam" ftype="bam" />
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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32 <param name="ref_file" value="hxb2_pol.fas" ftype="fasta" />
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33 <output name="output" >
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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34 <assert_contents>
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35 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/>
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dcd43b402eb3 planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
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36 <has_text_matching expression="hxb2_pol\s606\s.\sa\sc\s100\sPASS\sDP=157;AC=12;AF=0.0764" />
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37 <has_text_matching expression="hxb2_pol\s812\s.\sg\sa\s58\sPASS\sDP=634;AC=10;AF=0.0158" />
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38 <has_text_matching expression="hxb2_pol\s2278\s.\sc\st\s54\sPASS\sDP=557;AC=9;AF=0.0162" />
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39 </assert_contents>
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40 </output>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44
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45 Nucleotide Variants
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46 ===================
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48 Call nucleotide variants for a given BAM file and a supplied reference file.
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50 ]]></help>
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51 <expand macro="citations" />
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52 </tool>