Mercurial > repos > iuc > mothur_trim_flows

annotate trim.flows.xml @ 3:5c31047be933 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:30:46 -0500
parents 054074503e50
children 40d7b488661e
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f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_trim_flows" name="Trim.flows" version="@WRAPPER_VERSION@.0">
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>partition by barcode, trim to length, cull by length and mismatches</description>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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3 <macros>
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4 <import>macros.xml</import>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
1
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
1
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9 <command><![CDATA[
3
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10 @SHELL_OPTIONS@
1
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11
3
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12 ## create symlinks to input datasets
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 ln -s '$flow' flow.dat &&
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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14 #if $oligo.add == "yes":
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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15 ln -s '$oligo.oligos' oligo.oligos.dat &&
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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16 #end if
0
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17
3
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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18 echo 'trim.flows(
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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19 flow=flow.dat,
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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20 minflows=$minflows,
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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21 maxflows=$maxflows,
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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22 #if $maxhomop:
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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23 maxhomop=$maxhomop,
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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24 #end if
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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25 order=$order,
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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26 signal=$signal,
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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27 noise=$noise,
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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28 #if $oligo.add == "yes":
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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29 oligos=oligo.oligos.dat,
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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30 bdiffs=$oligo.bdiffs,
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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31 pdiffs=$oligo.pdiffs,
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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32 tdiffs=$oligo.tdiffs,
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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33 ldiffs=$oligo.ldiffs,
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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34 sdiffs=$oligo.sdiffs,
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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35 #end if
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36 fasta=$fasta,
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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37 processors='\${GALAXY_SLOTS:-8}'
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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38 )'
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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39 | sed 's/ //g' ## mothur trips over whitespace
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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40 | mothur
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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41 | tee mothur.out.log
5c31047be933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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42
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43 ## prevent these two files from being gathered into collection
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44 && mv flow.trim.flow flow.trim
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45 && mv flow.scrap.flow flow.scrap
0
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46 ]]></command>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 <inputs>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 <param name="flow" type="data" format="mothur.sff.flow" label="flow - flowgram data" help="Use sffinfo to generate flow data from an sff file"/>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 <conditional name="oligo">
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 <param name="add" type="select" label="Trim with an oligos file?" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file">
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51 <option value="no">no</option>
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52 <option value="yes">yes</option>
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53 </param>
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54 <when value="no"/>
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55 <when value="yes">
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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56 <param name="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/>
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57 <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (default 0)"/>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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58 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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59 <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)"/>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 <param name="ldiffs" type="integer" value="0" min="0" label="ldiffs - total number of differences to allow in linker sequence (default 0)"/>
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61 <param name="sdiffs" type="integer" value="0" min="0" label="sdiffs - total number of differences to allow in spacer sequence (default 0)"/>
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62 </when>
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63 </conditional>
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64 <param name="minflows" type="integer" value="450" min="0" label="minflows - Minimum number of flows that each sequence must contain to make it in to a &quot;trim&quot; file. (default 450)" help="(Quince uses 360)"/>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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65 <param name="maxflows" type="integer" value="450" min="0" label="maxflows - Maximum number of flows after which all other flows should be ignored (default 450)" help="(Quince uses 360 for GSFLX and 720 for Titanium)"/>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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66 <param name="maxhomop" type="integer" value="" optional="true" label="maxhomop - Maximum homopolymers" help=""/>
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67 <param name="signal" type="float" value="0.5" min="0.0" max="1.0" label="signal - treat any intensity signal greater than this threshold as a real signal" help="Optional. Between 0 an 1. Default .5"/>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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68 <param name="noise" type="float" value="0.7" min="0.0" max="1.0" label="noise - treat any intensity signal less than this threshold as noise" help="Optional. Between 0 and 1. Default .7"/>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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69 <param name="order" type="select" label="order - flow order for nucleotides in the sequencer" help="default is A, was TACG. Also accepts B or I">
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70 <option value="A" selected="true"> A (TACG) </option>
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71 <option value="B"> B </option>
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72 <option value="I"> I </option>
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73 </param>
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74 <param name="fasta" type="boolean" truevalue="true" falsevalue="false" checked="false" label="fasta - translate the flowgram data to fasta sequence format"/>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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75 </inputs>
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76 <outputs>
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77 <expand macro="logfile-output"/>
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78 <data name="trim_flow" format="mothur.sff.flow" from_work_dir="flow.trim" label="${tool.name} on ${on_string}: trim.flow"/>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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79 <data name="scrap_flow" format="mothur.sff.flow" from_work_dir="flow.scrap" label="${tool.name} on ${on_string}: scrap.flow"/>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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80 <data name="flow_files" format="tabular" from_work_dir="flow.flow.files" label="${tool.name} on ${on_string}: flow.files"/>
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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81 <data name="flow_fasta" format="fasta" from_work_dir="flow.flow.fasta" label="${tool.name} on ${on_string}: flow.fasta">
f60bc63d84cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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82 <filter>fasta</filter>
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83 </data>
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84 <collection name="flow_oligos" type="list" label="${tool.name} on ${on_string}: oligos.flow">
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85 <filter>oligo['add'] == 'yes'</filter>
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86 <discover_datasets pattern="flow\.(?P&lt;designation&gt;.*)\.flow" format="mothur.sff.flow"/>
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87 </collection>
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88 </outputs>
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89 <tests>
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90 <test><!-- test with defaults -->
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91 <param name="flow" value="mock.flow" ftype="mothur.sff.flow"/>
1
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92 <output name="trim_flow" md5="6850bb59570822aec6cd7aa7ce4675c4" ftype="mothur.sff.flow"/>
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93 <output name="scrap_flow" md5="e5d39459c28f5e7245bae7c509f05cba" ftype="mothur.sff.flow"/>
0
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94 <output name="flow_files" ftype="tabular">
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95 <assert_contents>
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96 <has_text text="flow"/>
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97 </assert_contents>
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98 </output>
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99 <expand macro="logfile-test"/>
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100 </test>
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101 <test><!-- test with oligos file and fasta output -->
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102 <param name="flow" value="testflow.flow" ftype="mothur.sff.flow"/>
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103 <param name="add" value="yes"/>
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104 <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
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105 <param name="order" value="I"/>
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106 <param name="fasta" value="true"/>
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107 <param name="pdiffs" value="10"/>
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108 <param name="bdiffs" value="10"/>
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109 <output name="trim_flow" md5="fdb1634899e8a6f8490ace953382591e" ftype="mothur.sff.flow"/>
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110 <output name="scrap_flow" md5="dd2497eb1e3da8d513d2b0bc111cdf11" ftype="mothur.sff.flow"/>
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111 <output name="flow_files" ftype="tabular">
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112 <assert_contents>
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113 <has_text text="flow"/>
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114 </assert_contents>
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115 </output>
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116 <output_collection name="flow_oligos" count="2">
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117 <element name="F003D006" md5="5ea6613d7aa26f87ca9b983152e14a4b" ftype="mothur.sff.flow"/>
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118 </output_collection>
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119 <output name="flow_fasta" md5="0725967a9ed731c049d48ea876b0e308" ftype="fasta"/>
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120 <expand macro="logfile-test"/>
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121 </test>
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122 </tests>
3
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123 <help><![CDATA[
0
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124
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125 @MOTHUR_OVERVIEW@
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126
1
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127 **Command Documentation**
0
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128
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129 The trim.flows_ command is analogous to the trim.seqs command, except that it uses the flowgram data that comes bundled in the sff file that is generated by 454 sequencing. It's primary usage is as a preliminary step to running shhh.seqs. Chris Quince has a series of perl scripts that fulfill a similar role [1]. This command will allow you to partition your flowgram data by sample based on the barcode, trim the flows to a specified length range, and cull sequences that are too short or have too many mismatches to barcodes and primers.
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130
1
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131 .. _trim.flows: https://www.mothur.org/wiki/Trim.flows
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132
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133 ]]></help>
0
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134 <expand macro="citations"/>
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135 </tool>