Mercurial > repos > iuc > presto_collapseseq

annotate presto_collapseseq.xml @ 0:d1a1b738c119 draft

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author iuc
date Wed, 30 May 2018 15:36:25 -0400
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d1a1b738c119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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1 <tool id="presto_collapseseq" name="pRESTO CollapseSeq" version="@PRESTO_VERSION@">
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2 <description>Remove/collapse duplicate sequences</description>
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3
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4 <macros>
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5 <import>presto_macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements"/>
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9
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10 <version_command>CollapseSeq.py --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ln -s '$fastq_in' in.fastq &&
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13 CollapseSeq.py
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14 -s in.fastq
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15 -n '$n'
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16 --uf $uf
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17 --cf $cf
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18 --act $act
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19 $inner
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20 $keepmiss
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21
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22 #if $representative.select_by == "by_min"
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23 --minf '$minf'
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24 #end if
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25 #if $representative.select_by == "by_max"
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26 --maxf '$maxf'
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27 #end if
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28
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29 --outname=tmp
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30 #if $capture_log
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31 --log '$log_out'
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32 #end if
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33 ]]></command>
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34
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35 <inputs>
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36 <param argument="-s" name="fastq_in" type="data" format="fastq"
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37 label="Input FASTQ file" help="FASTQ file of sequences."/>
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38 <param argument="-n" type="integer" value="0" label="Max Missing"
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39 help="Maximum number of missing nucleotides to consider for collapsing sequences. A sequence will be considered undetermined if it contains too many missing nucleotides."/>
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40 <param argument="--uf" type="text" value="" label="Unique Field(s)" help="Space-separated list of fields to match reads by."/>
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41 <param argument="--cf" type="text" value="" label="Copy Field(s)" help="Space-separated list of fields to copy into the target sequence headers.">
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42 <expand macro="text-regex-validator"/>
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43 </param>
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44 <param argument="--act" type="text" value="" label="Action(s)" help="Space-separated list of actions to take on Copy Field(s).">
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45 <expand macro="text-regex-validator"/>
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46 </param>
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47 <param argument="--inner" type="boolean" value="false" truevalue="--inner" falsevalue="" label="Inner" help="If true, trim off any missing/undetermined bases from the ends of reads after collapsing."/>
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48 <param argument="--keepmiss" type="boolean" value="false" truevalue="--keepmiss" falsevalue="" label="Keep Missing"
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49 help="If specified, sequences with more missing characters than the threshold set by the -n parameter will be written to the unique sequence output file with a DUPCOUNT=1 annotation. If not specified, such sequences will be written to a separate file."/>
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50 <conditional name="representative">
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51 <param name="select_by" type="select">
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52 <option value="first">First Sequence</option>
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53 <option value="by_min">By field minimum value</option>
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54 <option value="by_max">By field maximum value</option>
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55 </param>
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56 <when value="first"></when>
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57 <when value="by_min">
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58 <param argument="--minf" type="text" value="" label="Field Name" help="Specifies the field whose minimum value determines the retained sequence."/>
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59 </when>
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60 <when value="by_max">
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61 <param argument="--maxf" type="text" value="" label="Field Name" help="Specifies the field whose maximum value determines the retained sequence."/>
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62 </when>
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63 </conditional>
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64 <expand macro="presto-log-param"/>
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65 </inputs>
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66
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67 <outputs>
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68 <data name="fastq_out" format="fastq" from_work_dir="tmp_collapse-unique.fastq"/>
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69 <expand macro="presto-log-output"/>
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70 </outputs>
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71
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72 <tests>
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73 <test>
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74 <param name="fastq_in" value="presto_collapseseq_test_in.fastq"/>
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75 <param name="n" value="0"/>
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76 <param name="uf" value="PRCONS CREGION"/>
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77 <param name="cf" value="CONSCOUNT"/>
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78 <param name="act" value="sum"/>
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79 <param name="inner" value="true"/>
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80 <param name="keepmiss" value="true"/>
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81 <output name="fastq_out" file="presto_collapseseq_test_output.fastq" sort="true"/>
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82 </test>
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83 </tests>
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84
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85 <help><![CDATA[
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86 Removes/collapses duplicate sequences from FASTQ files.
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87
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88 See the `pRESTO online help <@PRESTO_URL_BASE@/CollapseSeq.html>`_ for more information.
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89
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90 @HELP_NOTE@
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91 ]]></help>
d1a1b738c119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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92 <expand macro="citations" />
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93 </tool>