Mercurial > repos > jjohnson > contig_annotation_tool
annotate cat_bins.xml @ 2:9a01840eac52 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 6b978e61a7f66160f2577d907f52dd641f103986-dirty
author | jjohnson |
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date | Mon, 25 Nov 2019 15:09:24 -0500 |
parents | 86cd2e70b0dc |
children | 18ece3d5bcde |
rev | line source |
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1
86cd2e70b0dc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 2ed43d093253670323e67fda6db0cbb2ece98aad-dirty
jjohnson
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1 <tool id="cat_bins" name="CAT bins" version="@VERSION@.0"> |
0
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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2 <description>annotate with taxonomic classification</description> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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3 <macros> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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4 <import>macros.xml</import> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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5 </macros> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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6 <expand macro="requirements" /> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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7 <expand macro="version_command" /> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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8 <command detect_errors="exit_code"><![CDATA[ |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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9 #set $bin_dir = None |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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10 #if len($mags) > 1: |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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11 #set $bin_dir = 'inputs' |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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12 mkdir -p $bin_dir && |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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13 #for mag in $mags: |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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14 ln -s '$mag' $bin_dir/ && |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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15 #end for |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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16 #end if |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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17 CAT |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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18 #if $bin_dir |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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19 bins -s '.dat' -b $bin_dir |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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20 #else |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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21 bin -b '$mags' |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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22 #end if |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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23 @CAT_DB@ |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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24 @USE_INTERMEDIATES@ |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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25 @CUSTOM_SETTINGS@ |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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26 && @TXT2TSV@ *.ORF2LCA.txt *.bin2classification.txt |
2
9a01840eac52
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 6b978e61a7f66160f2577d907f52dd641f103986-dirty
jjohnson
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27 #if len($mags) > 1: |
9a01840eac52
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 6b978e61a7f66160f2577d907f52dd641f103986-dirty
jjohnson
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28 #set pat = '$' + '{i/concatenated./}' |
9a01840eac52
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 6b978e61a7f66160f2577d907f52dd641f103986-dirty
jjohnson
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29 && (for i in *.concatenated.*; do ln -s "\$i" "${pat}"; done) |
9a01840eac52
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 6b978e61a7f66160f2577d907f52dd641f103986-dirty
jjohnson
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30 #end if |
0
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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31 @ADD_NAMES@ |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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32 @SUMMARISE@ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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33 ]]></command> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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34 <inputs> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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35 <param name="mags" type="data" format="fasta" multiple="true" label="metagenome assembled genomes (MAGs/bins)"/> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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36 <expand macro="cat_db" /> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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37 <expand macro="use_intermediates" /> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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38 <expand macro="custom_settings" /> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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39 <expand macro="add_names" /> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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40 <expand macro="summarise" /> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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41 <expand macro="select_bat_outputs" /> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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42 </inputs> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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43 <outputs> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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44 <expand macro="outputs" /> |
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45 </outputs> |
ad7507073c3f
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46 <tests> |
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47 <test> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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48 <param name="mags" ftype="fasta" value="genome3.fna"/> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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49 <expand macro="test_catdb"/> |
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50 <param name="select_outputs" value="contig2classification"/> |
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51 <output name="contig2classification"> |
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52 <assert_contents> |
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53 <has_text text="1639" /> |
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54 </assert_contents> |
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55 </output> |
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56 </test> |
1
86cd2e70b0dc
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57 <test> |
0
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58 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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59 <expand macro="test_catdb"/> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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60 <param name="select_outputs" value="contig2classification"/> |
ad7507073c3f
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61 <output name="contig2classification"> |
ad7507073c3f
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62 <assert_contents> |
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63 <has_text text="666" /> |
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64 <has_text text="1639" /> |
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65 </assert_contents> |
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66 </output> |
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67 </test> |
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68 </tests> |
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69 <help><![CDATA[ |
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70 **CAT bin or bins** |
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71 Classify metagenomics assembled genomes. |
ad7507073c3f
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72 |
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73 @COMMON_HELP@ |
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74 ]]></help> |
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75 <expand macro="citations" /> |
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76 </tool> |