Mercurial > repos > iuc > semibin_concatenate_fasta

annotate concatenate_fasta.xml @ 0:dcc81bfe5f6a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
author iuc
date Fri, 14 Oct 2022 21:51:40 +0000
parents
children e6bc3455940e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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1 <tool id="semibin_concatenate_fasta" name="SemiBin: Concatenate fasta files" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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2 <description>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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3 for multi-sample binning
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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4 </description>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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5 <macros>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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6 <import>macros.xml</import>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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7 </macros>
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8 <expand macro="biotools"/>
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9 <expand macro="requirements"/>
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10 <expand macro="version"/>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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11 <command detect_errors="exit_code"><![CDATA[
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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12 #import re
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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13 #for $e in $input_fasta
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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14 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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15 #if $e.ext.endswith(".gz")
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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16 gunzip -c '$e' > '${identifier}.fasta' &&
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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17 #else
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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18 ln -s '$e' '${identifier}.fasta' &&
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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19 #end if
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20 #end for
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21
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22 SemiBin concatenate_fasta
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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23 --input-fasta *.fasta
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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24 --output 'output'
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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25 --separator '$separator'
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26 -m $min_len
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27 ]]></command>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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28 <inputs>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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29 <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz" label="Contig sequences"/>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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30 <expand macro="separator"/>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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31 <expand macro="concat_min_len"/>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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32 </inputs>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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33 <outputs>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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34 <data name="fasta" format="fasta" from_work_dir="output/concatenated.fa" />
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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35 </outputs>
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36 <tests>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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37 <test expect_num_outputs="1">
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38 <param name="input_fasta" ftype="fasta" value="input_single.fasta,input_single_2.fasta,input_single_3.fasta"/>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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39 <param name="separator" value=":"/>
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40 <param name="min_len" value="0"/>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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41 <output name="fasta" ftype="fasta">
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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42 <assert_contents>
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43 <has_text text=">input_single:g1k_0"/>
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44 <has_text text=">input_single_3:g4k_7"/>
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45 <has_text text=">input_single_2:g1k_0"/>
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46 </assert_contents>
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47 </output>
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48 </test>
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49 </tests>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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50 <help><![CDATA[
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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51 @HELP_HEADER@
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52
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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53 Inputs
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54 ======
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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55
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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56 @HELP_INPUT_FASTA@
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57
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58 Outputs
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59 =======
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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60
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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61 - One fasta with all contigs
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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62
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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63 ]]></help>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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64 <expand macro="citations"/>
dcc81bfe5f6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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65 </tool>