Mercurial > repos > iuc > khmer_filter_abundance

annotate filter-abund.xml @ 9:b86562b4f3fd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 11:47:42 +0000
parents 97f65399e30d
children
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1 <tool id="khmer_filter_abundance" name="khmer: Filter reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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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 <expand macro="bio_tools"/>
0
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6 <macros>
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7 <token name="@BINARY@">filter-abund.py</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements" />
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11 <expand macro="stdio" />
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12 <expand macro="version" />
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13 <command><![CDATA[
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14 set -u &&
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15 @LINK_SEQUENCES@
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16 mkdir output && cd output &&
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17 @BINARY@
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18 --cutoff=${cutoff}
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19 ${variable_coverage}
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20 @THREADS@
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21 ${input_countgraph_filename}
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22 @USE_SEQUENCES@
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23 ]]>
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24 </command>
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25 <inputs>
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26 <expand macro="input_sequences_filenames" />
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27 <param argument="--variable_coverage" name="variable_coverage" type="boolean" checked="false" truevalue="--variable-coverage" falsevalue=""
0
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28 label="Variable coverage"
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29 help="Only trim when a sequence has high enough coverage; median abundance > 20" />
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30 <param argument="--cutoff" name="cutoff" type="integer" value="2" label="Cutoff"
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31 help="Trim at k-mers below this abundance" />
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32 <expand macro="input_countgraph_filename" />
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33 </inputs>
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34 <outputs>
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35 <expand macro="output_sequences" extension="abundfilt"/>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="inputs" value="test-abund-read-2.fa" />
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40 <param name="input_countgraph_filename"
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41 value="test-abund-read-2.oxlicg" ftype="oxlicg" />
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42 <output_collection name="sequences" type="list">
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43 <element name="test-abund-read-2.fa">
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44 <assert_contents>
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45 <has_text text="GGTTGACGGGGCTCAGGG" />
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46 </assert_contents>
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47 </element>
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48 </output_collection>
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49 </test>
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50 <test>
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51 <param name="inputs" value="test-abund-read-2.fa" />
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52 <param name="input_countgraph_filename"
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53 value="test-abund-read-2.oxlicg" ftype="oxlicg" />
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54 <param name="cutoff" value="1" />
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55 <output_collection name="sequences" type="list">
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56 <element name="test-abund-read-2.fa">
0
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57 <assert_contents>
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58 <has_text text="GGTTGACGGGGCTCAGGG" />
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59 </assert_contents>
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60 </element>
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61 </output_collection>
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62 </test>
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63 </tests>
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64 <help><![CDATA[
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65 Trims fastq/fasta sequences at k-mers of a given abundance based on a provided k-mer countgraph
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66
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67 If the input sequences are from RNAseq or metagenome sequencing then
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68 `--variable-coverage` should be used.
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69
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70 @HELP_FOOTER@
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71 ]]>
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72 </help>
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73 <citations>
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74 <expand macro="software-citation" />
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75 <expand macro="counting-citation" />
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76 </citations>
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77 </tool>