Mercurial > repos > iuc > mothur_degap_seqs

annotate degap.seqs.xml @ 5:a7fced14ce99 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a
author iuc
date Fri, 03 Aug 2018 14:23:34 -0400
parents f643cbd3a967
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_degap_seqs" name="Degap.seqs" version="@WRAPPER_VERSION@.0">
7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Remove gap characters from sequences</description>
7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
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4 <import>macros.xml</import>
7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
f643cbd3a967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$fasta' fasta.dat &&
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14
2
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15 echo 'degap.seqs(
f643cbd3a967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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16 fasta=fasta.dat
f643cbd3a967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 )'
f643cbd3a967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 | sed 's/ //g' ## mothur trips over whitespace
f643cbd3a967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 | mothur
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20 | tee mothur.out.log
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7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 ]]></command>
7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22 <inputs>
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23 <param name="fasta" type="data" format="fasta" label="fasta - Dataset"/>
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24 <expand macro="param-savelog"/>
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7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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25 </inputs>
7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 <outputs>
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27 <expand macro="logfile-output"/>
7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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28 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.ng.fasta" label="${tool.name} on ${on_string}: fasta"/>
7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 </outputs>
7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 <tests>
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31 <test>
7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ng.fasta"/>
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f643cbd3a967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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34 <param name="savelog" value="true"/>
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7cd72305d496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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35 <expand macro="logfile-test"/>
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36 </test>
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37 </tests>
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38 <help>
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39 <![CDATA[
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41 @MOTHUR_OVERVIEW@
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42
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43 **Command Documentation**
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44
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45 The degap.seqs_ command reads a fasta file and outputs a fasta containing the sequences after all gap characters are removed.
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46
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47 .. _degap.seqs: https://www.mothur.org/wiki/Degap.seqs
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48
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49 v1.21.0: Updated to Mothur 1.33
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50
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51 ]]>
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52 </help>
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53 <expand macro="citations"/>
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54 </tool>