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annotate aacoverage.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="aacoverage" name="Amino Acid Coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>Builds an aa census and returns its coverage</description>
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18aad692772a planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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3 <macros>
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4 <import>macros.xml</import>
18aad692772a planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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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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8
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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 aacoverage '${input_bam.name}' $ref_file $input_genes -o output.csv
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14 ]]></command>
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15 <inputs>
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16 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
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17 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
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18 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
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19 </inputs>
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20 <outputs>
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21 <data format="csv" name="output" from_work_dir="output.csv" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input_bam" value="align.bam" />
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26 <param name="ref_file" value="hxb2_pol.fas" />
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27 <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
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28 <output name="output" >
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29 <assert_contents>
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30 <has_text text="frame: 0" />
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31 <has_text text="1,0" />
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32 <has_text text="948,1" />
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33 </assert_contents>
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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34 </output>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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39 Amino Acid Coverage
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40 ===================
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71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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42 Builds an amino acid census and returns its coverage.
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44 **Output**
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46 A file with one entry per line with the AA position and the coverage at the position.
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48 ]]></help>
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49 <expand macro="citations" />
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50 </tool>