annotate filter-abund.xml @ 8:97f65399e30d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 14ea2dc5ef36219c908ed64b256794711ce7b902"
author iuc
date Tue, 23 Mar 2021 21:30:15 +0000
parents 8c6433857aa8
children b86562b4f3fd
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1 <tool id="khmer_filter_abundance" name="khmer: Filter reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>
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3 by minimal k-mer abundance
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4 </description>
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5 <macros>
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6 <token name="@BINARY@">filter-abund.py</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
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10 <expand macro="stdio" />
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11 <expand macro="version" />
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12 <command><![CDATA[
7
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13 set -u &&
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14 @LINK_SEQUENCES@
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15 mkdir output && cd output &&
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16 @BINARY@
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17 --cutoff=${cutoff}
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18 ${variable_coverage}
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19 @THREADS@
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20 ${input_countgraph_filename}
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21 @USE_SEQUENCES@
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22 ]]>
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23 </command>
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24 <inputs>
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25 <expand macro="input_sequences_filenames" />
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26 <param argument="--variable_coverage" name="variable_coverage" type="boolean" checked="false" truevalue="--variable-coverage" falsevalue=""
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27 label="Variable coverage"
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28 help="Only trim when a sequence has high enough coverage; median abundance > 20" />
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29 <param argument="--cutoff" name="cutoff" type="integer" value="2" label="Cutoff"
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30 help="Trim at k-mers below this abundance" />
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31 <expand macro="input_countgraph_filename" />
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32 </inputs>
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33 <outputs>
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34 <expand macro="output_sequences" extension="abundfilt"/>
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="inputs" value="test-abund-read-2.fa" />
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39 <param name="input_countgraph_filename"
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40 value="test-abund-read-2.oxlicg" ftype="oxlicg" />
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41 <output_collection name="sequences" type="list">
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42 <element name="test-abund-read-2.fa">
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43 <assert_contents>
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44 <has_text text="GGTTGACGGGGCTCAGGG" />
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45 </assert_contents>
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46 </element>
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47 </output_collection>
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48 </test>
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49 <test>
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50 <param name="inputs" value="test-abund-read-2.fa" />
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51 <param name="input_countgraph_filename"
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52 value="test-abund-read-2.oxlicg" ftype="oxlicg" />
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53 <param name="cutoff" value="1" />
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54 <output_collection name="sequences" type="list">
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55 <element name="test-abund-read-2.fa">
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56 <assert_contents>
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57 <has_text text="GGTTGACGGGGCTCAGGG" />
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58 </assert_contents>
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59 </element>
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60 </output_collection>
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61 </test>
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62 </tests>
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63 <help><![CDATA[
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64 Trims fastq/fasta sequences at k-mers of a given abundance based on a provided k-mer countgraph
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65
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66 If the input sequences are from RNAseq or metagenome sequencing then
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67 `--variable-coverage` should be used.
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68
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69 @HELP_FOOTER@
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70 ]]>
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71 </help>
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72 <citations>
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73 <expand macro="software-citation" />
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74 <expand macro="counting-citation" />
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75 </citations>
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76 </tool>