Mercurial > repos > iuc > ampvis2_export_fasta

annotate export_fasta.xml @ 2:0ddd34d51029 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
author iuc
date Mon, 18 Dec 2023 09:42:04 +0000
parents e10b5eebd415
children
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3c3c359d9b85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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1 <tool id="ampvis2_export_fasta" name="ampvis2 export fasta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="header"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript '$rscript'
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9 ]]></command>
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10 <configfiles>
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11 <configfile name="rscript"><![CDATA[
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12 library(ampvis2, quietly = TRUE)
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13 data <- readRDS("$data")
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14 amp_export_fasta(data, filename = "$output", tax = $tax)
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15 ]]></configfile>
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16 </configfiles>
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17 <inputs>
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18 <expand macro="rds_input_macro"/>
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19 <param argument="tax" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Add taxonomic strings to the output"/>
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20 </inputs>
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21 <outputs>
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22 <data name="output" format="fasta"/>
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23 </outputs>
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24 <tests>
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25 <!-- defaults -->
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26 <test expect_num_outputs="1">
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27 <param name="data" value="AalborgWWTPs-complete.rds" ftype="ampvis2"/>
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28 <output name="output" value="AalborgWWTPs.fa" ftype="fasta"/>
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29 </test>
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30 <!-- tax -->
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31 <test expect_num_outputs="1">
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32 <param name="data" value="AalborgWWTPs-complete.rds" ftype="ampvis2"/>
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33 <param name="tax" value="true"/>
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34 <output name="output" ftype="fasta">
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35 <assert_contents>
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36 <has_text text=">OTU_2397; k__Bacteria; p__Chloroflexi; c__Anaerolineae; o__Anaerolineales; f__Anaerolineaceae; g__uncultured; s__"/>
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37 <has_size value="125478"/>
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38 </assert_contents>
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39 </output>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 What it does
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44 ============
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45
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46 Export sequences from an ampvis2 object and optionally add taxonomy to the fasta header lines.
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47
3c3c359d9b85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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48 The Galaxy tool calls the `amp_export_fasta
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49 <https://kasperskytte.github.io/ampvis2/reference/amp_export_fasta.html>`_ function
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50 of the ampvis2 package.
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51
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52 Input
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53 =====
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54
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55 @HELP_RDS_INPUT@
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56
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57 In order to work the ampvis2 rds data set needs to contain sequence information.
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58
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59 Output
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60 ======
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61
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62 The sequences contained in the input as fasta.
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63
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64 ]]></help>
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65 <expand macro="citations"/>
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66 </tool>