Mercurial > repos > iuc > mothur_make_fastq

annotate make.fastq.xml @ 0:10e56de9ad1a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:37:49 -0400
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children 61b2c4a74b35
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10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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1 <tool profile="16.07" id="mothur_make_fastq" name="Make.fastq" version="@WRAPPER_VERSION@.0">
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Convert fasta and quality to fastq</description>
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3 <macros>
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iuc
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 ## create symlinks to input datasets
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10 ln -s "$fasta" fasta.dat &&
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$qfile" qfile.dat &&
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12
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13 echo 'make.fastq(
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 fasta=fasta.dat,
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 qfile=qfile.dat
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16 #if $chooseformat.use == "yes":
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17 ,format=${chooseformat.format}
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18 #end if
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19 )'
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20 | sed 's/ //g' ## mothur trips over whitespace
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21 | mothur
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22 ]]></command>
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23 <inputs>
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/>
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 <param name="qfile" type="data" format="qual454,qualillumina,qualsolid,qual" label="qfile - Sequence Quality file"/>
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 <conditional name="chooseformat">
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27 <param name="use" type="select" label="Choose quality format for your output sequences are" help="If none selected, this tool will keep the format of input qfile">
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 <option value="no" selected="true">no</option>
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 <option value="yes">yes</option>
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30 </param>
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31 <when value="yes">
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 <param name="format" type="select" optional="true" multiple="true">
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 <option value="sanger" selected="true">sanger</option>
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 <option value="illumina1.8+">Illumina 1.8+</option>
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 <option value="illumina">Illumina</option>
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 </param>
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37 </when>
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38 <when value="no"/>
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39 </conditional>
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40 </inputs>
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 <outputs>
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 <expand macro="logfile-output"/>
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 <data name="fastq" format="fasta" from_work_dir="fasta*.fastq" label="${tool.name} on ${on_string}: fastq">
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44 <change_format><!-- if set, chooseformat.format param should override qfile.ext format -->
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 <when input="qfile.ext" value="qual454" format="fastqsanger"/>
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46 <when input="qfile.ext" value="qualillumina" format="fastqillumina"/>
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 <when input="qfile.ext" value="qualsolid" format="fastqcssanger"/>
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 <when input="chooseformat.format" value="sanger" format="fastqsanger"/>
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 <when input="chooseformat.format" value="illumina1.8+" format="fastqsanger"/>
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 <when input="chooseformat.format" value="illumina" format="fastqillumina"/>
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51 </change_format>
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52 </data>
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53 </outputs>
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54 <tests>
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55 <test><!-- test defaults -->
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56 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
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57 <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
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58 <output name="fastq" md5="e77b78321620e300946c23147ad599fd" ftype="fastqsanger"/>
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59 <expand macro="logfile-test"/>
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60 </test>
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61 <test><!-- test with quality score format conversion -->
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62 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
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63 <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
10e56de9ad1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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64 <param name="use" value="yes"/>
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65 <param name="format" value="illumina"/>
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66 <output name="fastq" md5="c792253da205d4d1c66bc87a2969aa25" ftype="fastqillumina"/>
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67 <expand macro="logfile-test"/>
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68 </test>
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69 </tests>
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70 <help>
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71 <![CDATA[
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72
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73 @MOTHUR_OVERVIEW@
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74
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75 **Command Documenation**
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76
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77 The fastq.info_ command reads a fasta file and quality file and creates a fastq.
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78
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79
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80 .. _fastq.info: http://www.mothur.org/wiki/Make.fastq
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81 ]]>
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82 </help>
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83 <expand macro="citations"/>
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84 </tool>