Mercurial > repos > jjohnson > contig_annotation_tool

annotate cat_bins.xml @ 0:ad7507073c3f draft

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author jjohnson
date Sun, 24 Nov 2019 21:56:00 -0500
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children 86cd2e70b0dc
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0
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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1 <tool id="cat_bins" name="CAT bins" version="@VERSION.0">
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2 <description>annotate with taxonomic classification</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 #set $bin_dir = None
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10 #if len($mags) > 1:
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11 #set $bin_dir = 'inputs'
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12 mkdir -p $bin_dir &&
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13 #for mag in $mags:
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14 ln -s '$mag' $bin_dir/ &&
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15 #end for
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16 #end if
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17 CAT
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18 #if $bin_dir
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19 bins -s '.dat' -b $bin_dir
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20 #else
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21 bin -b '$mags'
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22 #end if
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23 @CAT_DB@
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24 @USE_INTERMEDIATES@
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25 @CUSTOM_SETTINGS@
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26 && @TXT2TSV@ *.ORF2LCA.txt *.bin2classification.txt
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27 @ADD_NAMES@
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28 @SUMMARISE@
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29 ]]></command>
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30 <inputs>
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31 <param name="mags" type="data" format="fasta" multiple="true" label="metagenome assembled genomes (MAGs/bins)"/>
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32 <expand macro="cat_db" />
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33 <expand macro="use_intermediates" />
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34 <expand macro="custom_settings" />
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35 <expand macro="add_names" />
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36 <expand macro="summarise" />
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37 <expand macro="select_bat_outputs" />
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38 </inputs>
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39 <outputs>
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40 <expand macro="outputs" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="mags" ftype="fasta" value="genome3.fna"/>
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45 <expand macro="test_catdb"/>
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46 <param name="select_outputs" value="contig2classification"/>
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47 <output name="contig2classification">
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48 <assert_contents>
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49 <has_text text="1639" />
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50 </assert_contents>
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51 </output>
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52 </test>
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53 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
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54 <expand macro="test_catdb"/>
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55 <param name="select_outputs" value="contig2classification"/>
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56 <output name="contig2classification">
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57 <assert_contents>
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58 <has_text text="666" />
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59 <has_text text="1639" />
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60 </assert_contents>
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61 </output>
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62 </test>
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63 </tests>
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64 <help><![CDATA[
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65 **CAT bin or bins**
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66 Classify metagenomics assembled genomes.
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67
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68 @COMMON_HELP@
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69 ]]></help>
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70 <expand macro="citations" />
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71 </tool>