Mercurial > repos > iuc > mothur_fastq_info

annotate fastq.info.xml @ 0:19316e7c4802 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:29:45 -0400
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children 1aa945e00ef2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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1 <tool profile="16.07" id="mothur_fastq_info" name="Fastq.info" version="@WRAPPER_VERSION@.0">
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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2 <description>Convert fastq to fasta and quality</description>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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3 <macros>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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4 <import>macros.xml</import>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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5 </macros>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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6 <expand macro="requirements"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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7 <expand macro="stdio"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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8 <expand macro="version_command"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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9 <command><![CDATA[
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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10 @SHELL_OPTIONS@
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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12 ## create symlinks to input datasets
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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13 ln -s "$fastq" fastq.dat &&
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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14 #if $oligo.add == "yes":
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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15 ln -s "$oligo.oligos" oligo.oligos.dat &&
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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16 #end if
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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18 echo 'fastq.info(
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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19 fastq=fastq.dat,
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 pacbio=$pacbio,
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 format=$format
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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22 #if $oligo.add == "yes":
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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23 ,oligos=oligo.oligos.dat
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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24 ,bdiffs=$oligo.bdiffs
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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25 ,pdiffs=$oligo.pdiffs
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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26 ,tdiffs=$oligo.tdiffs
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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27 ,ldiffs=$oligo.ldiffs
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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28 ,sdiffs=$oligo.sdiffs
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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29 #end if
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 )'
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 | sed 's/ //g' ## mothur trips over whitespace
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 | mothur
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 | tee mothur.out.log
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 ## rename some outputs
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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35 #if $oligo.add == "yes":
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 && mv fastq.scrap.fasta scrap.fasta
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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37 && mv fastq.scrap.qual scrap.qual
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 #end if
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 ]]></command>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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40 <inputs>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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41 <param name="fastq" type="data" format="fastq" label="fastq - Fastq Sequence file"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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42 <param name="pacbio" type="boolean" truevalue="true" falsevalue="false" checked="false" label="pacbio - if set to true, quality scores of 0 will results in a corresponding base of N"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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43 <param name="format" type="select" label="format of sequence">
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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44 <option value="sanger" selected="true">sanger</option>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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45 <option value="solexa">solexa</option>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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46 <option value="illumina">illumina</option>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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47 <option value="illumina1.8+">illumina1.8+</option>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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48 </param>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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49 <conditional name="oligo">
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50 <param name="add" type="select" label="Use oligos file?" help="a file that 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.">
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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54 <when value="yes">
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55 <param name="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/>
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56 <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (must be > 0; default 0)"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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57 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (must be > 0; default 0)"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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58 <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (must be > 0; default 0)"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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59 <param name="ldiffs" type="integer" value="0" min="0" label="ldiffs - total number of differences to allow in linker sequence (must be > 0; default 0)"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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60 <param name="sdiffs" type="integer" value="0" min="0" label="sdiffs - total number of differences to allow in spacer sequence (must be > 0; default 0)"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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61 </when>
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62 <when value="no"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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63 </conditional>
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64 </inputs>
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65 <outputs>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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66 <expand macro="logfile-output"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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67 <data name="fasta_out" format="fasta" from_work_dir="fastq*.fasta" label="${tool.name} on ${on_string}: fasta"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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68 <data name="qfile_out" format="qual454" from_work_dir="fastq*.qual" label="${tool.name} on ${on_string}: qual"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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69 <data name="fastq_scrap_out" format="fastq" from_work_dir="fastq*.scrap.fastq" label="${tool.name} on ${on_string}: fastq scrap">
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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70 <filter>oligos</filter>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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71 </data>
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72 <data name="fasta_scrap_out" format="fasta" from_work_dir="scrap.fasta" label="${tool.name} on ${on_string}: fasta scrap">
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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73 <filter>oligos</filter>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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74 </data>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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75 <data name="qfile_scrap_out" format="qual454" from_work_dir="scrap.qual" label="${tool.name} on ${on_string}: qual scrap">
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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76 <filter>oligos</filter>
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77 </data>
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78 </outputs>
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79 <tests>
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80 <test>
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81 <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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82 <param name="pacbio" value="false"/>
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83 <param name="format" value="sanger"/>
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84 <param name="add" value="no"/>
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85 <output name="fasta_out" md5="88c573d00181be6dd519a0c9599f8b0c"/>
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86 <output name="qfile_out" md5="d382c496c583b1501666459757cabbe3"/>
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87 <expand macro="logfile-test"/>
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88 </test>
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89 <test>
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90 <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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91 <param name="pacbio" value="false"/>
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92 <param name="format" value="sanger"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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93 <param name="add" value="yes"/>
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94 <param name="oligos" value="GQY1XT001.oligos"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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95 <param name="bdiffs" value="1"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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96 <param name="pdiffs" value="3"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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97 <param name="tdiffs" value="3"/>
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98 <param name="ldiffs" value="3"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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99 <param name="sdiffs" value="7"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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100 <output name="fasta_out" md5="88c573d00181be6dd519a0c9599f8b0c" ftype="fasta"/>
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101 <output name="qfile_out" md5="d382c496c583b1501666459757cabbe3" ftype="qual454"/>
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102 <output name="fastq_scrap_out" md5="37a280b8af54af2a0a52b2eba1e58933" ftype="fastq"/>
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103 <output name="fasta_scrap_out" md5="88c573d00181be6dd519a0c9599f8b0c" ftype="fasta"/>
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104 <output name="qfile_scrap_out" md5="96c2f7ea3cf6336d50bef2c087280c01" ftype="qual454"/>
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105 <expand macro="logfile-test"/>
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106 </test>
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107 <test>
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108 <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/>
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109 <param name="pacbio" value="false"/>
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110 <param name="format" value="sanger"/>
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111 <param name="add" value="yes"/>
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112 <param name="oligos" value="HMPv5-v3_1368-1369.oligos"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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113 <param name="bdiffs" value="1"/>
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114 <param name="pdiffs" value="3"/>
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115 <param name="tdiffs" value="3"/>
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116 <param name="ldiffs" value="3"/>
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117 <param name="sdiffs" value="7"/>
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118 <output name="fasta_out" md5="88c573d00181be6dd519a0c9599f8b0c"/>
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119 <output name="qfile_out" md5="d382c496c583b1501666459757cabbe3"/>
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120 <output name="fastq_scrap_out" md5="37a280b8af54af2a0a52b2eba1e58933"/>
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121 <output name="fasta_scrap_out" md5="88c573d00181be6dd519a0c9599f8b0c"/>
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122 <output name="qfile_scrap_out" md5="96c2f7ea3cf6336d50bef2c087280c01"/>
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123 <expand macro="logfile-test"/>
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124 </test>
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125 </tests>
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126 <help>
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127 <![CDATA[
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128
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129 @MOTHUR_OVERVIEW@
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130
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131 **Command Documentation**
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132
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133 The fastq.info_ command reads a fastq file and creates a fasta and quality file.
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134
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135
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136 .. _fastq.info: https://www.mothur.org/wiki/Fastq.info
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137 ]]>
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138 </help>
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139 <expand macro="citations"/>
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140 </tool>