Mercurial > repos > iuc > freyja_variants

annotate freyja_variants.xml @ 1:1f467ed22412 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
author iuc
date Fri, 07 Jul 2023 05:50:46 +0000
parents 08c2d81e7942
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08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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1 <tool id="freyja_variants" name="Freyja: Call variants"
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2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
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3 profile="@PROFILE@">
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4 <description>
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5 and get sequencing depth information
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6 </description>
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7 <macros>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="biotools"/>
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11 <expand macro="requirements"/>
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12 <expand macro="version"/>
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13 <command detect_errors="exit_code"><![CDATA[
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14 ln -s '$bam_file' 'bam_file' &&
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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15 ln -s '$ref_file' 'ref_file' &&
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16 freyja variants
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17 'bam_file'
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18 --variants variants
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19 --depths '$depths'
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20 --ref 'ref_file'
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21 ]]></command>
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22 <inputs>
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23 <param name="bam_file" type="data" format="bam" label="BAM file"
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24 help="After primer trimming and alignment to reference genome."/>
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25 <param name="ref_file" argument="--ref" type="data" format="fasta"
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26 label="Reference sequence file"
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27 help="Note that the reference should match the fasta file used for alignment."/>
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28 </inputs>
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29 <outputs>
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30 <data name="variants" format="tabular" label="${tool.name} on ${on_string}: Variant call"
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31 from_work_dir="variants.tsv">
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32 </data>
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33 <data name="depths" format="tabular" label="${tool.name} on ${on_string}: Sequencing depth"
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34 from_work_dir="depths.tsv">
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35 </data>
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36 </outputs>
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37 <tests>
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38 <test expect_num_outputs="2">
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39 <param name="bam_file" value="test.bam"/>
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40 <param name="ref_file" value="NC_045512_Hu-1.fasta"/>
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41 <output name="variants" ftype="tabular">
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42 <assert_contents>
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43 <has_text text="REF_CODON"/>
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44 <has_text text="NC_045512.2"/>
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45 </assert_contents>
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46 </output>
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47 <output name="depths" ftype="tabular">
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48 <assert_contents>
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49 <has_text text="NC_045512.2"/>
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50 </assert_contents>
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51 </output>
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52 </test>
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53 </tests>
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54 <help><![CDATA[
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55 @HELP_HEADER@
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56
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57 Information about **freyja variants** method
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58 ============================================
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59
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60 The method uses both samtools and iVar.
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61
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62 .. class:: warningmark
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63
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64 Note that the reference should match the fasta file used for alignment.
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65
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66 Outputs
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67 =======
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68
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69 We get both variant call and sequencing depth information with this command.
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70
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71 ]]></help>
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72 <expand macro="citations"/>
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73 </tool>