Mercurial > repos > iuc > khmer

annotate filter-abund.xml @ 0:0187f18785a3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
author iuc
date Sat, 17 Oct 2015 04:02:33 -0400
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0
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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1 <tool id="gedlab-khmer-filter-abund" name="Filter by abundance" version="@WRAPPER_VERSION@-5">
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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2 <description>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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3 Trims fastq/fasta sequences at k-mers of a given abundance
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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4 based on a provided k-mer countgraph
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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5 </description>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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6 <macros>
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7 <token name="@BINARY@">filter-abund.py</token>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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8 <import>macros.xml</import>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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9 </macros>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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10 <expand macro="requirements" />
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11 <expand macro="stdio" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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12 <expand macro="version" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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13 <command><![CDATA[
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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14 set -xu &&
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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15 #for $num, $input in enumerate($inputs)
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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16 ln -s ${input} filter-abund-sequence-${num} &&
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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17 #end for
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18 mkdir output && cd output &&
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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19 @BINARY@
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20 --cutoff=${cutoff}
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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21 ${variable_coverage}
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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22 @THREADS@
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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23 ${input_countgraph_filename}
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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24 ../filter-abund-sequence*
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25 ]]>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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26 </command>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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27 <inputs>
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28 <expand macro="input_sequences_filenames" />
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29 <param name="variable_coverage" type="boolean" checked="false" truevalue="--variable-coverage" falsevalue=""
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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30 label="Variable coverage"
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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31 help="Only trim when a sequence has high enough coverage; median abundance > 20 (--variable_coverage)" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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32 <param name="cutoff" type="integer" value="2" label="Cutoff"
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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33 help="Trim at k-mers below this abundance. (--cutoff)" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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34 <expand macro="input_countgraph_filename" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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35 </inputs>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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36 <outputs>
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37 <collection name="filter-abund-sequences" type="list">
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38 <discover_datasets pattern="__name__" directory="output" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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39 </collection>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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40 </outputs>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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41 <tests>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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42 <test>
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43 <param name="inputs" value="test-abund-read-2.fa" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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44 <param name="input_countgraph_filename"
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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45 value="test-abund-read-2.oxlicg" ftype="oxlicg" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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46 <output_collection name="filter-abund-sequences" type="list">
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47 <element name="filter-abund-sequence-0.abundfilt">
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48 <assert_contents>
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49 <has_text text="GGTTGACGGGGCTCAGGG" />
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50 </assert_contents>
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51 </element>
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52 </output_collection>
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53 </test>
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54 <test>
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55 <param name="inputs" value="test-abund-read-2.fa" />
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56 <param name="input_countgraph_filename"
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57 value="test-abund-read-2.oxlicg" ftype="oxlicg" />
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58 <param name="cutoff" value="1" />
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59 <output_collection name="filter-abund-sequences" type="list">
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60 <element name="filter-abund-sequence-0.abundfilt">
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61 <assert_contents>
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62 <has_text text="GGTTGACGGGGCTCAGGG" />
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63 </assert_contents>
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64 </element>
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65 </output_collection>
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66 </test>
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67 </tests>
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68 <help><![CDATA[
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69 Trim sequences at a minimum k-mer abundance.
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70
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71 If the input sequences are from RNAseq or metagenome sequencing then
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72 `--variable-coverage` should be used.
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73
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74 @HELP_FOOTER@
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75 ]]>
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76 </help>
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77 <citations>
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78 <expand macro="software-citation" />
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79 <expand macro="counting-citation" />
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80 </citations>
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81 </tool>