Mercurial > repos > iuc > metaphlan

annotate metaphlan.xml @ 13:ef65b083bd0c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
author iuc
date Sun, 08 Sep 2024 06:59:00 +0000
parents 1a037928504c
children 740fd2d16a28
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13
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1 <tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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2 <description>to profile the composition of microbial communities</description>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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3 <macros>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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4 <import>macros.xml</import>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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5 <xml name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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6 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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7 <param argument="--tax_lev" type="select" label="Taxonomic level for the relative abundance output">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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8 <option value="a" selected="true">All taxonomic levels</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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9 <option value="k">Kingdoms only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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10 <option value="p">Phyla only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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11 <option value="c">Classes only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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12 <option value="o">Orders only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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13 <option value="f">Families only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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14 <option value="g">Genera only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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15 <option value="s">Species only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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16 </param>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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17 <when value="a">
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1a037928504c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
iuc
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18 <param name="split_levels" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a report for each taxonomic level?" help="It will be in addition to the default output"/>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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19 </when>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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20 <when value="k"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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21 <when value="p"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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22 <when value="c"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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23 <when value="o"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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24 <when value="f"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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25 <when value="g"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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26 <when value="s"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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27 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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28 </xml>
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ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
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29 <token name="@FILE_FORMATS@">fastq,fastq.gz,fastq.bz2,fasta,fasta.gz</token>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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30 </macros>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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31 <expand macro="edam_ontology"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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32 <expand macro="requirements"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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33 <version_command>metaphlan -v</version_command>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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34 <command detect_errors="aggressive"><![CDATA[
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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35 #if $inputs.in.selector == "raw"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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36 #if $inputs.in.raw_in.selector == "single"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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37 #set full_ext=$inputs.in.raw_in.in.datatype.file_ext
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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38 #if $full_ext.endswith("gz")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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39 #set $file_path="in"
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b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
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40 zcat '$inputs.in.raw_in.in' > '$file_path' &&
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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41 #else if $full_ext.endswith("bz2")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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42 #set $file_path="in"
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b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
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43 bzcat '$inputs.in.raw_in.in' > '$file_path' &&
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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44 #else
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
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45 #set $file_path="'%s'" % $inputs.in.raw_in.in
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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46 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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47 #else if $inputs.in.raw_in.selector == "multiple"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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48 #set full_ext=$inputs.in.raw_in.in[0].datatype.file_ext
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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49 #set file_path=""
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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50 #set sep=""
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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51 #for $i, $f in enumerate($inputs.in.raw_in.in)
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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52 #if $f.datatype.file_ext != $full_ext
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b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
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53 echo "Different datatypes for input files" &&
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
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54 exit 1
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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55 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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56 #if $full_ext.endswith("gz")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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57 #set fp="input_%s" % ($i)
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
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58 zcat '$f' > '$fp' &&
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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59 #else if $full_ext.endswith("bz2")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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60 #set fp="input_%s" % ($i)
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
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61 bzcat '$f' > '$fp' &&
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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62 #else
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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63 #set fp=$f
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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64 #end if
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
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65 #set $file_path+="'%s%s'" % ($sep, $fp)
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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66 #set $sep=","
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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67 #end for
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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68 #else if $inputs.in.raw_in.selector == "paired"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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69 #set full_ext=$inputs.in.raw_in.in_f.datatype.file_ext
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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70 #if $full_ext != $inputs.in.raw_in.in_r.datatype.file_ext
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
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71 echo "Different datatypes for input paired-end files" &&
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
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72 exit 1
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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73 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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74 #if $full_ext.endswith("gz")
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
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75 zcat '$inputs.in.raw_in.in_f' > 'in_f' &&
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
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76 zcat '$inputs.in.raw_in.in_r' > 'in_r' &&
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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77 #else if $full_ext.endswith("bz2")
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
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78 bzcat '$inputs.in.raw_in.in_f' > 'in_f' &&
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
79 bzcat '$inputs.in.raw_in.in_r' > 'in_r' &&
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
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80 #set file_path="-1 in_f -2 in_r"
13
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
81 ln -s '$inputs.in.raw_in.in_f' 'in_f' &&
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
82 ln -s '$inputs.in.raw_in.in_r' 'in_r' &&
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
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diff changeset
83 #end if
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
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84 ## paired data has by default no special treatment, i.e. it is given as comma separated list
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85 ## except iff paired subsampling where -1 and -2 must be used
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
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diff changeset
86 #if $subsample.selector == 'paired'
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
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87 #set file_path="-1 in_f -2 in_r"
0
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88 #else
13
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89 #set file_path="in_f,in_r"
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90 #end if
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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91 #else if $inputs.in.raw_in.selector == "paired_collection"
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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92 #set full_ext=$inputs.in.raw_in.in.forward.ext
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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93 #if $full_ext != $inputs.in.raw_in.in.reverse.ext
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94 echo "Different datatypes for input paired-end files" &&
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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95 exit 1
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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96 #end if
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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97 #if $full_ext.endswith("gz")
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98 zcat '$inputs.in.raw_in.in.forward' > 'in_f' &&
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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99 zcat '$inputs.in.raw_in.in.reverse' > 'in_r' &&
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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100 #else if $full_ext.endswith("bz2")
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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101 bzcat '$inputs.in.raw_in.in.forward' > 'in_f' &&
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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102 bzcat '$inputs.in.raw_in.in.reverse' > 'in_r' &&
13
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103 #else
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104 ln -s '$inputs.in.raw_in.in.forward' 'in_f' &&
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
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105 ln -s '$inputs.in.raw_in.in.reverse' 'in_r' &&
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
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106 #end if
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
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107 #if $subsample.selector == 'paired'
11
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108 #set file_path="-1 in_f -2 in_r"
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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109 #else
13
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110 #set file_path="in_f,in_r"
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111 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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112 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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113
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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114 #if $full_ext.startswith("fastq")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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115 #set ext='fastq'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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116 #else if $full_ext.startswith("fasta") and $full_ext.endswith(("gz","bz2"))
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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117 #set ext='fasta'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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118 #else
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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119 #set ext=$full_ext
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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120 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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121 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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122
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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123 #if $inputs.db.db_selector == "history"
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124 mkdir 'ref_db' &&
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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125 bowtie2-build --large-index '$inputs.db.bowtie2db' 'ref_db/custom_db' &&
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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126 python
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127 '$__tool_directory__/customizemetadata.py'
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128 transform_json_to_pkl
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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129 --json '$inputs.db.mpa_pkl'
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130 --pkl 'ref_db/custom_db.pkl' &&
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131 #end if
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132
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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133 metaphlan
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134 #if $inputs.in.selector == "raw"
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135 $file_path
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136 --input_type '$ext'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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137 --read_min_len $inputs.in.read_min_len
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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138 --bt2_ps '$inputs.in.mapping.bt2_ps'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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139 --min_mapq_val $inputs.in.mapping.min_mapq_val
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140 #if $ext == "sam"
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141 --nreads \$(cat '$file_path' | grep -c -v '^@')
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142 #end if
0
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143 #else
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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144 '$inputs.in.in'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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145 --input_type '$inputs.in.selector'
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146 #if $inputs.in.selector == "sam"
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147 --nreads \$(cat '$inputs.in.in' | grep -c -v '^@')
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148 #end if
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149 #end if
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150 #if $inputs.db.db_selector == "cached"
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151 --bowtie2db '$inputs.db.cached_db.fields.path'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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152 --index '$inputs.db.cached_db.fields.dbkey'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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153 #else
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154 --bowtie2db 'ref_db/'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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155 --index 'custom_db'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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156 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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157 -t '$analysis.analysis_type.t'
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158 #if $analysis.analysis_type.t == "rel_ab" or $analysis.analysis_type.t == "rel_ab_w_read_stats"
1
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159 --tax_lev '$analysis.analysis_type.tax_lev.tax_lev'
0
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160 #else if $analysis.analysis_type.t == "clade_specific_strain_tracker"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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161 --clade '$analysis.analysis_type.clade'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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162 #if str($analysis.analysis_type.min_ab) != ''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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163 --min_ab $analysis.analysis_type.min_ab
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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164 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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165 #else if $analysis.analysis_type.t == "marker_ab_table" and str($analysis.analysis_type.nreads) != ''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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166 --nreads $$analysis.analysis_type.nreads
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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diff changeset
167 #else if $analysis.analysis_type.t == "marker_pres_table" and str($analysis.analysis_type.pres_th) != ''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
168 --pres_th $analysis.analysis_type.pres_th
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
169 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
170 --min_cu_len $analysis.min_cu_len
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
171 #if str($analysis.min_alignment_len) != ''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
172 --min_alignment_len $analysis.min_alignment_len
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
173 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
174 #if 'add_viruses' in $analysis.organism_profiling
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
175 --add_viruses
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
176 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
177 #if 'ignore_eukaryotes' in $analysis.organism_profiling
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
178 --ignore_eukaryotes
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
179 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
180 #if 'ignore_bacteria' in $analysis.organism_profiling
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
181 --ignore_bacteria
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
182 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
183 #if 'ignore_archaea' in $analysis.organism_profiling
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
184 --ignore_archaea
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
185 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
186 --stat_q $analysis.stat_q
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
187 --perc_nonzero $analysis.perc_nonzero
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
188 #if $analysis.ignore_markers
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
189 --ignore_markers '$analysis.ignore_markers'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
190 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
191 $analysis.avoid_disqm
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
192 --sample_id_key '$out.sample_id_key'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
193 --sample_id '$out.sample_id'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
194 $out.use_group_representative
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
195 $out.legacy_output
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
196 $out.CAMI_format_output
10
289b3807e80c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit b8bc892a6d5eeae0b78c33058b532fcd52208179
iuc
parents: 8
diff changeset
197 $out.unclassified_estimation
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
198 -o '$output_file'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
199 --bowtie2out 'bowtie2out'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
200 -s '$sam_output_file'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
201 --biom '$biom_output_file'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
202 --nproc \${GALAXY_SLOTS:-4}
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
203 #if $viral_analysis.profile_vsc
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
204 $viral_analysis.profile_vsc
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
205 --vsc_out '$vcs_breath_coverage'
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
206 --vsc_breadth $viral_analysis.vsc_breadth
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
207 #end if
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
208
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
209 #if $subsample.selector != "no"
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
210 #if $subsample.selector == "single"
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
211 --subsampling $subsample.subsampling
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
212 #else
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
213 --subsampling_paired $subsample.subsampling_paired
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
214 #end if
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
215 $subsample.mapping_subsampling
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
216 #if $subsample.subsampling_seed
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
217 --subsampling_seed $subsample.subsampling_seed
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
218 #end if
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
219 --subsampling_output subsampled.out
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
220 #end if
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
221
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
222 #if $test == "false"
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
223 --offline
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
224 #end if
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
225
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
226 #if $inputs.in.selector == "raw"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
227 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
228 mv 'bowtie2out' '$bowtie2out'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
229 #end if
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
230
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
231
8
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
232 #if $analysis.analysis_type.t in ['rel_ab', 'rel_ab_w_read_stats']
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
233 #if $analysis.analysis_type.tax_lev.tax_lev == 'a' and $analysis.analysis_type.tax_lev.split_levels
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
234 &&
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
235 mkdir 'split_levels'
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
236 &&
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
237 python '$__tool_directory__/formatoutput.py'
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
238 split_levels
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
239 --metaphlan_output '$output_file'
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
240 --outdir 'split_levels'
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
241 $out.legacy_output
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
242 #end if
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
243 #end if
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
244
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
245 #if $out.krona_output
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
246 &&
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
247 python '$__tool_directory__/formatoutput.py'
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
248 format_for_krona
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
249 --metaphlan_output '$output_file'
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
250 --krona_output '$krona_output_file'
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
251 #end if
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
252 ]]></command>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
253 <inputs>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
254 <section name="inputs" title="Inputs" expanded="true">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
255 <conditional name="in">
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256 <param name="selector" type="select" label="Input(s)">
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257 <option value="raw" selected="true">Fasta/FastQ file(s) with microbiota reads</option>
0
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258 <option value="sam">Externally BowTie2-mapped SAM file</option>
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259 <option value="bowtie2out">Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run</option>
0
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260 </param>
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261 <when value="raw">
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262 <conditional name="raw_in">
2
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263 <param name="selector" type="select" label="Fasta/FastQ file(s) with microbiota reads">
0
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264 <option value="single" selected="true">One single-end file</option>
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265 <option value="multiple">Multiple single-end files</option>
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266 <option value="paired_collection">Paired-end collection</option>
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267 <option value="paired">Paired-end files</option>
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268 </param>
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269 <when value="single">
2
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270 <param name="in" type="data" format="@FILE_FORMATS@" label="Single-end Fasta/FastQ file with microbiota reads"/>
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271 </when>
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272 <when value="multiple">
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273 <param name="in" type="data" format="@FILE_FORMATS@" label="Single-end Fasta/FastQ files with microbiota reads" multiple="true"/>
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274 </when>
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275 <when value="paired_collection">
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276 <param name="in" type="data_collection" format="@FILE_FORMATS@" label="Paired-end Fasta/FastQ file with microbiota reads" collection_type="paired"/>
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277 </when>
0
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278 <when value="paired">
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279 <param name="in_f" type="data" format="@FILE_FORMATS@" label="Forward paired-end Fasta/FastQ file with microbiota reads"/>
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280 <param name="in_r" type="data" format="@FILE_FORMATS@" label="Reverse paired-end Fasta/FastQ file with microbiota reads"/>
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281 </when>
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282 </conditional>
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283 <param argument="--read_min_len" type="integer" value="70" label="Minimum length of the reads to be considered when parsing the input file"/>
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284 <section name="mapping" title="Mapping" expanded="true">
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285 <param argument="--bt2_ps" type="select" label="Presets options for BowTie2" help="Applied only with FASTA files">
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286 <option value="sensitive">Sensitive</option>
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287 <option value="very-sensitive" selected="true">Very sensitive</option>
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288 <option value="sensitive-local">Sensitive local</option>
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289 <option value="very-sensitive-local">Very sensitive local</option>
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290 </param>
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291 <param argument="--min_mapq_val" type="integer" value="5" label="Minimum mapping quality value (MAPQ)"/>
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292 </section>
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293 </when>
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294 <when value="sam">
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295 <param name="in" type="data" format="sam" label="Externally BowTie2-mapped SAM file" help="BowTie2 needs to be used first to map microbiota reads"/>
0
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296 </when>
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297 <when value="bowtie2out">
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298 <param name="in" type="data" format="tabular" label="Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run" help="File needs to be generated with MetaPhlAn versions &gt;3.0"/>
0
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299 </when>
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300 </conditional>
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301 <conditional name="db">
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302 <param name="db_selector" type="select" label="Database with clade-specific marker genes">
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303 <option value="cached" selected="true">Locally cached</option>
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304 <option value="history">From history</option>
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305 </param>
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306 <when value="cached">
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307 <param name="cached_db" type="select" label="Cached database with clade-specific marker genes">
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308 <options from_data_table="@IDX_DATA_TABLE@">
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309 <filter type="static_value" column="4" value="@IDX_VERSION@"/>
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310 <validator message="No compatible MetaPhlAn database is available" type="no_options"/>
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311 </options>
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312 </param>
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313 </when>
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314 <when value="history">
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315 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>
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316 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associated to the database with clade-specific marker genes from history"/>
0
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317 </when>
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318 </conditional>
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319 </section>
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320 <section name="analysis" title="Analysis" expanded="true">
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321 <conditional name="analysis_type">
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322 <param argument="-t" type="select" label="Type of analysis to perform">
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323 <option value="rel_ab" selected="true">rel_ab: Profiling a microbiota in terms of relative abundances</option>
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324 <option value="rel_ab_w_read_stats">rel_ab_w_read_stats: Profiling a microbiota in terms of relative abundances and estimate the number of reads comming from each clade</option>
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325 <option value="reads_map">reads_map: Mapping from reads to clades (only reads hitting a marker)</option>
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326 <option value="clade_profiles">clade_profiles: Normalized marker counts for clades with at least a non-null marker</option>
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327 <option value="clade_specific_strain_tracker">clade_specific_strain_tracker: List of markers present for a specific clade and all its subclades</option>
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328 <option value="marker_ab_table">marker_ab_table: Normalized marker counts (only when &gt; 0.0 and normalized by microbiota size if number of reads is specified)</option>
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329 <option value="marker_counts">marker_counts: Non-normalized marker counts (use with extreme caution)</option>
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330 <option value="marker_pres_table">marker_pres_table: List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
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331 </param>
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332 <when value="rel_ab">
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333 <expand macro="tax_lev"/>
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334 </when>
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335 <when value="rel_ab_w_read_stats">
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336 <expand macro="tax_lev"/>
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337 </when>
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338 <when value="reads_map"/>
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339 <when value="clade_profiles"/>
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340 <when value="clade_specific_strain_tracker">
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341 <param argument="--clade" type="text" value="" label="Clade for which to extract list of markers present" help="Markers are also extracted for subclades"/>
0
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342 <param argument="--min_ab" type="float" optional="true" label="The minimum percentage abundance for the clade"/>
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343 </when>
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344 <when value="marker_ab_table">
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345 <param argument="--nreads" type="integer" optional="true" label="Total number of reads in the original microbiota" help="It is used for normalizing the length-normalized counts with the microbiota size as well. No normalization applied if the value is not specified"/>
0
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346 </when>
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347 <when value="marker_counts"/>
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348 <when value="marker_pres_table">
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349 <param argument="--pres_th" type="integer" optional="true" label="Threshold for calling a marker present"/>
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350 </when>
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351 </conditional>
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352 <param argument="--min_cu_len" type="integer" value="2000" label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances"/>
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353 <param argument="--min_alignment_len" type="integer" optional="true" label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded."/>
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354 <param name="organism_profiling" type="select" optional="true" label="Organisms to profile" multiple="true">
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355 <option value="add_viruses" selected="true">Profile viral organisms (add_viruses)</option>
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356 <option value="ignore_eukaryotes">Ignore eukaryotic organisms (ignore_eukaryotes)</option>
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357 <option value="ignore_bacteria">Ignore bacteria organisms (ignore_bacteria)</option>
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358 <option value="ignore_archaea">Ignore archea organisms (ignore_archaea)</option>
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359 </param>
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360 <param argument="--stat" type="select" label="Statistical approach for converting marker abundances into clade abundances">
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361 <option value="avg_g">avg_g: Clade global (i.e. normalizing all markers together) average (avg_g)</option>
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362 <option value="avg_l">avg_l: Average of length-normalized marker counts</option>
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363 <option value="tavg_g" selected="true">tavg_g: Truncated clade global average at --stat_q quantile</option>
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364 <option value="tavg_l">tavg_l: Truncated average of length-normalized marker counts (at --stat_q)</option>
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365 <option value="wavg_g">wavg_g: Winsorized clade global average (at --stat_q)</option>
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366 <option value="wavg_l">wavg_l: Winsorized average of length-normalized marker counts (at --stat_q)</option>
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367 <option value="med">med: Median of length-normalized marker counts</option>
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368 </param>
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369 <param argument="--stat_q" type="float" value="0.2" label="Quantile value for the robust average"/>
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370 <param argument="--perc_nonzero" type="float" value="0.33" label="Percentage of markers with a non zero relative abundance for misidentify a species"/>
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371 <param argument="--ignore_markers" type="data" format="txt,tabular" optional="true" label="File containing a list of markers to ignore" help="One marker per line"/>
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372 <param argument="--avoid_disqm" type="boolean" truevalue="--avoid_disqm" falsevalue="" checked="true" label="Deactivate the procedure of disambiguating the quasi-markers based on the marker abundance pattern found in the sample?" help="It is generally recommended to keep the disambiguation procedure in order to minimize false positives"/>
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373 </section>
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374 <conditional name="subsample">
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375 <param name="selector" type="select" label="Subsample" help="Subsampling only works for fastq input">
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376 <option value="no">No</option>
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377 <option value="single">Yes: specify number of reads</option>
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378 <option value="paired">Yes: specify number of paired reads</option>
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379 </param>
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380 <when value="no"/>
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381 <when value="single">
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382 <param argument="--subsampling" type="integer" min="1" value="" label="Sumbsample reads" help="Specify the number of reads to be considered"/>
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383 <expand macro="subsample_common"/>
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384 </when>
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385 <when value="paired">
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386 <param argument="--subsampling_paired" type="integer" min="1" value="" label="Sumbsample reads" help="Specify the number of paired reads to be considered. For N there will be floor(N/2) reads selected from the forward and reverse reads each."/>
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387 <expand macro="subsample_common"/>
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388 </when>
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389 </conditional>
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390 <conditional name="viral_analysis">
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391 <param argument="--profile_vsc" type="select" label="Profile Viruses with VSCs approach">
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392 <option value="--profile_vsc">Yes (requires FASTQ input and reference data with VSG fasta)</option>
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393 <option value="" selected="true">No</option>
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394 </param>
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395 <when value="--profile_vsc">
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396 <param argument="--vsc_breadth" type="float" min="0" max="1" value="0.75" label="Minimum Breadth of Coverage" help="Minimum coverage (fraction) for a Viral Group to be reported."/>
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397 </when>
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398 <when value=""/>
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399 </conditional>
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400 <section name="out" title="Outputs" expanded="true">
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401 <param argument="--sample_id_key" type="text" value="SampleID" label="Sample ID key for this analysis"/>
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402 <param argument="--sample_id" type="text" value="Metaphlan_Analysis" label="Sample ID for this analysis"/>
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403 <param argument="--use_group_representative" type="boolean" truevalue="--use_group_representative" falsevalue="" checked="false" label="Use a species as representative for species groups?"/>
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404 <param argument="--legacy-output" type="boolean" truevalue="--legacy-output" falsevalue="" checked="false" label="Old MetaPhlAn2 two columns output?"/>
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405 <param argument="--CAMI_format_output" type="boolean" truevalue="--CAMI_format_output" falsevalue="" checked="false" label="Report the profiling using the CAMI output format?"/>
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406 <param argument="--unclassified_estimation" type="boolean" truevalue="--unclassified_estimation" falsevalue="" checked="false" label="Scale relative abundances to the number of reads mapping to known clades in order to estimate unknowness?"/>
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407 <param name="krona_output" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output for Krona?"/>
0
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408 </section>
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409 <!-- enabling this in tests will allow metaphlan to download reference data (we do this only with the smallish TOY DB) -->
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410 <param name="test" type="hidden" value="false"/>
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411 </inputs>
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412 <outputs>
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diff changeset
413 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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414 <data name="bowtie2out" format="tabular" label="${tool.name} on ${on_string}: Bowtie2 output">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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diff changeset
415 <filter>inputs['in']['selector'] == "raw"</filter>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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diff changeset
416 </data>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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diff changeset
417 <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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diff changeset
418 <filter>inputs['in']['selector'] == "raw"</filter>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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419 </data>
12
1a037928504c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
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parents: 11
diff changeset
420 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file"/>
1a037928504c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
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diff changeset
421 <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels">
1
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iuc
parents: 0
diff changeset
422 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="split_levels/" format="tabular"/>
8
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
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diff changeset
423 <filter>analysis['analysis_type']['t'] in ['rel_ab', 'rel_ab_w_read_stats'] and analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
424 </collection>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
425 <data name="krona_output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances for Krona">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
426 <filter>out['krona_output']</filter>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
427 </data>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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parents: 10
diff changeset
428 <data name="vcs_breath_coverage" format="tabular" label="${tool.name} on ${on_string}: VSCs breadth-of-coverage">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
429 <filter>viral_analysis['profile_vsc']</filter>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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parents: 10
diff changeset
430 </data>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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parents: 10
diff changeset
431 <data name="subsample_single" format="fastqsanger" from_work_dir="subsampled.out" label="${tool.name} on ${on_string}: Subsampled reads">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
432 <filter>subsample['selector'] == 'single'</filter>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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parents: 10
diff changeset
433 </data>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
434 <collection name="subsample_paired" type="paired" label="${tool.name} on ${on_string}: Subsampled paired reads">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
435 <data name="forward" format="fastqsanger" from_work_dir="subsampled.R1.out"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
436 <data name="reverse" format="fastqsanger" from_work_dir="subsampled.R2.out"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
437 <filter>subsample['selector'] == 'paired'</filter>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
438 </collection>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
439 </outputs>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
440 <tests>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
441 <!-- Single GZ file, Cached db -->
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
442 <test expect_num_outputs="6">
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
443 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
444 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
445 <param name="selector" value="raw"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
446 <conditional name="raw_in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
447 <param name="selector" value="single"/>
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
448 <param name="in" value="no_taxon_input.fasta"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
449 </conditional>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
450 <param name="read_min_len" value="70"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
451 <section name="mapping">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
452 <param name="bt2_ps" value="sensitive"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
453 <param name="min_mapq_val" value="5"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
454 </section>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
455 </conditional>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
456 <conditional name="db">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
457 <param name="db_selector" value="cached"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
458 <param name="cached_db" value="test-db-20210409"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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parents: 1
diff changeset
459 </conditional>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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parents: 1
diff changeset
460 </section>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
461 <section name="analysis">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
462 <conditional name="analysis_type">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
463 <param name="t" value="rel_ab"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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parents: 1
diff changeset
464 <conditional name="tax_lev">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
465 <param name="tax_lev" value="a"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
466 <param name="split_levels" value="true"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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parents: 1
diff changeset
467 </conditional>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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parents: 1
diff changeset
468 </conditional>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
469 <param name="min_cu_len" value="2000"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
470 <param name="organism_profiling" value="add_viruses"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
471 <param name="stat" value="avg_g"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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parents: 1
diff changeset
472 <param name="stat_q" value="0.2"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
473 <param name="perc_nonzero" value="0.33"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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parents: 1
diff changeset
474 <param name="avoid_disqm" value="true"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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parents: 1
diff changeset
475 </section>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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parents: 1
diff changeset
476 <section name="out">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
477 <param name="sample_id_key" value="SampleID"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
478 <param name="sample_id" value="Metaphlan_Analysis"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
479 <param name="use_group_representative" value="false"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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parents: 1
diff changeset
480 <param name="legacy_output" value="false"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
481 <param name="CAMI_format_output" value="false"/>
10
289b3807e80c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit b8bc892a6d5eeae0b78c33058b532fcd52208179
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parents: 8
diff changeset
482 <param name="unclassified_estimation" value="false"/>
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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parents: 1
diff changeset
483 <param name="krona_output" value="true"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
484 </section>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
485 <output name="output_file" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
486 <assert_contents>
5
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
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parents: 3
diff changeset
487 <has_text text="UNCLASSIFIED"/>
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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parents: 1
diff changeset
488 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
489 </output>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
490 <output name="bowtie2out" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
491 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
492 <not_has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
493 <has_n_lines n="2"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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parents: 1
diff changeset
494 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
495 </output>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
496 <output name="sam_output_file" ftype="sam">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
497 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
498 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
499 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
500 </output>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
501 <output name="biom_output_file" ftype="biom1">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
502 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
503 <not_has_text text="k__Bacteria"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
504 <not_has_text text="p__Actinobacteria"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
505 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
506 </output>
8
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
507 <output_collection name="levels" type="list">
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
508 <element name="all" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
509 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
510 <has_text text="class"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
511 <has_n_columns n="17"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
512 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
513 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
514 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
515 <element name="class" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
516 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
517 <has_text text="class_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
518 <not_has_text text="phylum_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
519 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
520 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
521 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
522 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
523 <element name="family" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
524 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
525 <has_text text="family_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
526 <not_has_text text="order"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
527 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
528 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
529 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
530 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
531 <element name="genus" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
532 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
533 <has_text text="genus_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
534 <not_has_text text="family"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
535 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
536 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
537 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
538 </element>
6
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
539 <element name="kingdom" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
540 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
541 <has_text text="kingdom_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
542 <has_n_columns n="3"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
543 <has_n_lines n="1"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
544 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
545 </element>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
546 <element name="order" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
547 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
548 <has_text text="order_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
549 <not_has_text text="class_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
550 <has_n_columns n="3"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
551 <has_n_lines n="1"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
552 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
553 </element>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
554 <element name="phylum" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
555 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
556 <has_text text="phylum_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
557 <not_has_text text="kingdom_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
558 <has_n_columns n="3"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
559 <has_n_lines n="1"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
560 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
561 </element>
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
562 <element name="species" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
563 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
564 <has_text text="species_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
565 <not_has_text text="genus"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
566 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
567 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
568 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
569 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
570 <element name="strains" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
571 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
572 <has_text text="strains_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
573 <not_has_text text="species_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
574 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
575 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
576 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
577 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
578 </output_collection>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
579 <output name="krona_output_file" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
580 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
581 <not_has_text text="k__Bacteria"/>
5
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
582 <has_n_lines n="1" delta="1"/>
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
583 <has_size value="1" delta="1"/>
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
584 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
585 </output>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
586 <assert_stderr>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
587 <has_text text="Downloading" negate="true"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
588 </assert_stderr>
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
589 </test>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
590 <!-- Single GZ file, Cached db -->
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
591 <test expect_num_outputs="6">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
592 <section name="inputs">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
593 <conditional name="in">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
594 <param name="selector" value="raw"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
595 <conditional name="raw_in">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
596 <param name="selector" value="single"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
597 <param name="in" value="SRS014464-Anterior_nares.fasta.gz"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
598 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
599 <param name="read_min_len" value="70"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
600 <section name="mapping">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
601 <param name="bt2_ps" value="sensitive"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
602 <param name="min_mapq_val" value="5"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
603 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
604 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
605 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
606 <param name="db_selector" value="cached"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
607 <param name="cached_db" value="test-db-20210409"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
608 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
609 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
610 <section name="analysis">
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
611 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
612 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
613 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
614 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
615 <param name="split_levels" value="true"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
616 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
617 </conditional>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
618 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
619 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
620 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
621 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
622 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
623 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
624 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
625 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
626 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
627 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
628 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
629 <param name="legacy_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
630 <param name="CAMI_format_output" value="false"/>
10
289b3807e80c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit b8bc892a6d5eeae0b78c33058b532fcd52208179
iuc
parents: 8
diff changeset
631 <param name="unclassified_estimation" value="false"/>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
632 <param name="krona_output" value="true"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
633 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
634 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
635 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
636 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
637 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
638 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
639 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-bowtie2out.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
640 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
641 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
642 <has_text text="37637__U2I1U8__N579_01580"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
643 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
644 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
645 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares.sam" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
646 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
647 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
648 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
649 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
650 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
651 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
652 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
653 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
654 </output>
12
1a037928504c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
iuc
parents: 11
diff changeset
655 <output_collection name="levels" type="list">
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
656 <element name="all" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
657 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
658 <has_text text="Gammaproteobacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
659 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
660 <has_n_columns n="17"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
661 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
662 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
663 <element name="class" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
664 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
665 <has_text text="class_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
666 <not_has_text text="phylum_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
667 <has_text text="Actinobacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
668 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
669 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
670 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
671 <element name="family" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
672 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
673 <has_text text="family_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
674 <not_has_text text="order"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
675 <has_text text="Propionibacteriaceae"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
676 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
677 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
678 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
679 <element name="genus" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
680 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
681 <has_text text="genus_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
682 <not_has_text text="family"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
683 <has_text text="Cutibacterium"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
684 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
685 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
686 </element>
6
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
687 <element name="kingdom" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
688 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
689 <has_text text="kingdom_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
690 <has_text text="Bacteria"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
691 <has_n_columns n="3"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
692 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
693 </element>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
694 <element name="order" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
695 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
696 <has_text text="order_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
697 <not_has_text text="class_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
698 <has_text text="Propionibacteriales"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
699 <has_n_columns n="3"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
700 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
701 </element>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
702 <element name="phylum" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
703 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
704 <has_text text="phylum_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
705 <not_has_text text="kingdom_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
706 <has_text text="Firmicutes"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
707 <has_n_columns n="3"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
708 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
709 </element>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
710 <element name="species" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
711 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
712 <has_text text="species_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
713 <not_has_text text="genus"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
714 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
715 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
716 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
717 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
718 <element name="strains" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
719 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
720 <has_text text="strains_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
721 <not_has_text text="species_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
722 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
723 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
724 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
725 </output_collection>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
726 <output name="krona_output_file" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
727 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
728 <not_has_text text="k__Bacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
729 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
730 <has_n_columns n="9"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
731 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
732 </output>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
733 <assert_stderr>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
734 <has_text text="Downloading" negate="true"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
735 </assert_stderr>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
736 </test>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
737 <!-- Multiple GZ file, Local db-->
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
738 <test expect_num_outputs="4">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
739 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
740 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
741 <param name="selector" value="raw"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
742 <conditional name="raw_in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
743 <param name="selector" value="multiple"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
744 <param name="in" value="SRS014464-Anterior_nares.fasta.gz,SRS014464-Anterior_nares.fasta.gz"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
745 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
746 <param name="read_min_len" value="70"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
747 <section name="mapping">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
748 <param name="bt2_ps" value="sensitive"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
749 <param name="min_mapq_val" value="5"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
750 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
751 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
752 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
753 <param name="db_selector" value="history"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
754 <param name="bowtie2db" value="test-db.fasta"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
755 <param name="mpa_pkl" value="test-db.json"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
756 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
757 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
758 <section name="analysis">
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
759 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
760 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
761 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
762 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
763 <param name="split_levels" value="false"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
764 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
765 </conditional>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
766 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
767 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
768 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
769 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
770 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
771 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
772 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
773 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
774 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
775 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
776 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
777 <param name="legacy_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
778 <param name="CAMI_format_output" value="false"/>
10
289b3807e80c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit b8bc892a6d5eeae0b78c33058b532fcd52208179
iuc
parents: 8
diff changeset
779 <param name="unclassified_estimation" value="false"/>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
780 <param name="krona_output" value="false"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
781 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
782 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
783 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
784 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
785 <has_text text="relative_abundance"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
786 <has_text text="NCBI_tax_id"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
787 <has_text text="clade_name"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
788 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
789 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
790 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
791 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
792 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
793 <has_text text="37637__U2I1U8__N579_01580"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
794 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
795 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
796 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares-two-inputs.sam" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
797 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
798 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
799 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
800 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
801 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
802 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
803 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
804 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
805 </output>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
806 <assert_stderr>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
807 <has_text text="Downloading" negate="true"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
808 </assert_stderr>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
809 </test>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
810 <!-- Paired GZ file, Cached db (note sumsample_paired and the included forward and reverse reads are counted separatelym because they are all statically defined) -->
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
811 <test expect_num_outputs="7">
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
812 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
813 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
814 <param name="selector" value="raw"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
815 <conditional name="raw_in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
816 <param name="selector" value="paired"/>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
817 <param name="in_f" value="SRS014464-Anterior_nares.fastq.gz"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
818 <param name="in_r" value="SRS014464-Anterior_nares.fastq.gz"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
819 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
820 <param name="read_min_len" value="70"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
821 <section name="mapping">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
822 <param name="bt2_ps" value="sensitive"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
823 <param name="min_mapq_val" value="5"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
824 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
825 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
826 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
827 <param name="db_selector" value="cached"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
828 <param name="cached_db" value="test-db-20210409"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
829 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
830 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
831 <section name="analysis">
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
832 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
833 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
834 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
835 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
836 <param name="split_levels" value="false"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
837 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
838 </conditional>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
839 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
840 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
841 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
842 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
843 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
844 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
845 </section>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
846 <conditional name="subsample">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
847 <param name="selector" value="paired"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
848 <param name="subsampling_paired" value="20257"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
849 <param name="subsampling_seed" value="42"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
850 </conditional>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
851 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
852 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
853 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
854 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
855 <param name="legacy_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
856 <param name="CAMI_format_output" value="false"/>
10
289b3807e80c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit b8bc892a6d5eeae0b78c33058b532fcd52208179
iuc
parents: 8
diff changeset
857 <param name="unclassified_estimation" value="false"/>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
858 <param name="krona_output" value="false"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
859 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
860 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
861 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
862 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
863 <has_text text="relative_abundance"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
864 <has_text text="NCBI_tax_id"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
865 <has_text text="clade_name"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
866 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
867 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
868 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
869 <assert_contents>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
870 <has_text text="HWI-EAS109_102883399:3:107:9938:7093/1"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
871 <has_text text="90240__A0A378QWM4__NCTC12877_00123"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
872 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
873 </output>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
874 <output name="sam_output_file" ftype="sam">
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
875 <assert_contents>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
876 <has_size min="52400" max="52600"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
877 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
878 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
879 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
880 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
881 <assert_contents>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
882 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
883 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
884 </output>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
885 <output_collection name="subsample_paired" type="paired">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
886 <element name="forward">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
887 <assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
888 <has_line_matching expression="^@.*" n="10128"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
889 </assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
890 </element>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
891 <element name="reverse">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
892 <assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
893 <has_line_matching expression="^@.*" n="10128"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
894 </assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
895 </element>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
896 </output_collection>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
897 <assert_stderr>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
898 <has_text text="Downloading" negate="true"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
899 </assert_stderr>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
900 </test>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
901 <!-- Paired GZ file as collection, Cached db (note sumsample_paired and the included forward and reverse reads are counted separatelym because they are all statically defined) -->
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
902 <test expect_num_outputs="7">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
903 <section name="inputs">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
904 <conditional name="in">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
905 <param name="selector" value="raw"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
906 <conditional name="raw_in">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
907 <param name="selector" value="paired_collection"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
908 <param name="in">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
909 <collection type="paired" name="pair">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
910 <element name="forward" value="SRS014464-Anterior_nares.fastq.gz"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
911 <element name="reverse" value="SRS014464-Anterior_nares.fastq.gz"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
912 </collection>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
913 </param>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
914 </conditional>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
915 <param name="read_min_len" value="70"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
916 <section name="mapping">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
917 <param name="bt2_ps" value="sensitive"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
918 <param name="min_mapq_val" value="5"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
919 </section>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
920 </conditional>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
921 <conditional name="db">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
922 <param name="db_selector" value="cached"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
923 <param name="cached_db" value="test-db-20210409"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
924 </conditional>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
925 </section>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
926 <section name="analysis">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
927 <conditional name="analysis_type">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
928 <param name="t" value="rel_ab"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
929 <conditional name="tax_lev">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
930 <param name="tax_lev" value="a"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
931 <param name="split_levels" value="false"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
932 </conditional>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
933 </conditional>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
934 <param name="min_cu_len" value="2000"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
935 <param name="organism_profiling" value="add_viruses"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
936 <param name="stat" value="avg_g"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
937 <param name="stat_q" value="0.2"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
938 <param name="perc_nonzero" value="0.33"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
939 <param name="avoid_disqm" value="true"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
940 </section>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
941 <conditional name="subsample">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
942 <param name="selector" value="paired"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
943 <param name="subsampling_paired" value="20257"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
944 <param name="subsampling_seed" value="42"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
945 </conditional>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
946 <section name="out">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
947 <param name="sample_id_key" value="SampleID"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
948 <param name="sample_id" value="Metaphlan_Analysis"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
949 <param name="use_group_representative" value="false"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
950 <param name="legacy_output" value="false"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
951 <param name="CAMI_format_output" value="false"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
952 <param name="unclassified_estimation" value="false"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
953 <param name="krona_output" value="false"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
954 </section>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
955 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
956 <assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
957 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
958 <has_text text="relative_abundance"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
959 <has_text text="NCBI_tax_id"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
960 <has_text text="clade_name"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
961 </assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
962 </output>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
963 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular" compare="sim_size">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
964 <assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
965 <has_text text="HWI-EAS109_102883399:3:107:9938:7093/1"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
966 <has_text text="90240__A0A378QWM4__NCTC12877_00123"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
967 </assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
968 </output>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
969 <output name="sam_output_file" ftype="sam">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
970 <assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
971 <has_size min="52400" max="52600"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
972 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
973 </assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
974 </output>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
975 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
976 <assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
977 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
978 </assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
979 </output>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
980 <output_collection name="subsample_paired" type="paired">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
981 <element name="forward">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
982 <assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
983 <has_line_matching expression="^@.*" n="10128"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
984 </assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
985 </element>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
986 <element name="reverse">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
987 <assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
988 <has_line_matching expression="^@.*" n="10128"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
989 </assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
990 </element>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
991 </output_collection>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
992 <assert_stderr>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
993 <has_text text="Downloading" negate="true"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
994 </assert_stderr>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
995 </test>
13
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
996 <!-- Paired fastq file as collection, Cached db -->
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
997 <test expect_num_outputs="4">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
998 <section name="inputs">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
999 <conditional name="in">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1000 <param name="selector" value="raw"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1001 <conditional name="raw_in">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1002 <param name="selector" value="paired_collection"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1003 <param name="in">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1004 <collection type="paired" name="pair">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1005 <element name="forward" value="SRS014464-Anterior_nares_mini.fastq" />
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1006 <element name="reverse" value="SRS014464-Anterior_nares_mini.fastq" />
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1007 </collection>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1008 </param>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1009 </conditional>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1010 <param name="read_min_len" value="70"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1011 <section name="mapping">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1012 <param name="bt2_ps" value="sensitive"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1013 <param name="min_mapq_val" value="5"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1014 </section>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1015 </conditional>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1016 <conditional name="db">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1017 <param name="db_selector" value="cached"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1018 <param name="cached_db" value="test-db-20210409"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1019 </conditional>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1020 </section>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1021 <section name="analysis">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1022 <conditional name="analysis_type">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1023 <param name="t" value="rel_ab"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1024 <conditional name="tax_lev">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1025 <param name="tax_lev" value="a"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1026 <param name="split_levels" value="false"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1027 </conditional>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1028 </conditional>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1029 <param name="min_cu_len" value="2000"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1030 <param name="organism_profiling" value="add_viruses"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1031 <param name="stat" value="avg_g"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1032 <param name="stat_q" value="0.2"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1033 <param name="perc_nonzero" value="0.33"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1034 <param name="avoid_disqm" value="true"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1035 </section>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1036 <conditional name="subsample">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1037 <param name="selector" value="no"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1038 </conditional>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1039 <section name="out">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1040 <param name="sample_id_key" value="SampleID"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1041 <param name="sample_id" value="Metaphlan_Analysis"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1042 <param name="use_group_representative" value="false"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1043 <param name="legacy_output" value="false"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1044 <param name="CAMI_format_output" value="false"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1045 <param name="unclassified_estimation" value="false"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1046 <param name="krona_output" value="false"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1047 </section>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1048 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1049 <assert_contents>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1050 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1051 <has_text text="relative_abundance"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1052 <has_text text="NCBI_tax_id"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1053 <has_text text="clade_name"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1054 </assert_contents>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1055 </output>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1056 <output name="bowtie2out" ftype="tabular">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1057 <assert_contents>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1058 <has_text text="HWI-EAS109_102883399:3:107:9938:7093/1"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1059 <has_text text="90240__A0A378QWM4__NCTC12877_00123"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1060 </assert_contents>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1061 </output>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1062 <output name="sam_output_file" ftype="sam">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1063 <assert_contents>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1064 <has_size min="8450" max="8550"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1065 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1066 </assert_contents>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1067 </output>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1068 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1069 <assert_contents>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1070 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1071 </assert_contents>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1072 </output>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1073 <assert_stderr>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1074 <has_text text="Downloading" negate="true"/>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1075 </assert_stderr>
ef65b083bd0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 8ab597f47a3a12919b55055380b6e725879cc5c0
iuc
parents: 12
diff changeset
1076 </test>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1077 <!-- SAM, cached DB -->
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1078 <test expect_num_outputs="2">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1079 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1080 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1081 <param name="selector" value="sam"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1082 <param name="in" value="SRS014464-Anterior_nares.sam"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1083 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1084 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1085 <param name="db_selector" value="cached"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1086 <param name="cached_db" value="test-db-20210409"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1087 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1088 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1089 <section name="analysis">
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1090 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1091 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1092 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1093 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1094 <param name="split_levels" value="false"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1095 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1096 </conditional>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1097 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1098 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1099 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1100 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1101 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1102 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1103 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1104 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1105 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1106 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1107 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1108 <param name="legacy_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1109 <param name="CAMI_format_output" value="false"/>
10
289b3807e80c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit b8bc892a6d5eeae0b78c33058b532fcd52208179
iuc
parents: 8
diff changeset
1110 <param name="unclassified_estimation" value="false"/>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1111 <param name="krona_output" value="false"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1112 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1113 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1114 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1115 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1116 <has_text text="relative_abundance"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1117 <has_text text="NCBI_tax_id"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1118 <has_text text="clade_name"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1119 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1120 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1121 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1122 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1123 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1124 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1125 </output>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1126 <assert_stderr>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1127 <has_text text="Downloading" negate="true"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1128 </assert_stderr>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1129 </test>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1130 <!-- bowtie2out, cached DB -->
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1131 <test expect_num_outputs="2">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1132 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1133 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1134 <param name="selector" value="bowtie2out"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1135 <param name="in" value="SRS014464-Anterior_nares-bowtie2out.tabular"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1136 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1137 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1138 <param name="db_selector" value="cached"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1139 <param name="cached_db" value="test-db-20210409"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1140 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1141 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1142 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1143 <param name="selector" value="bowtie2out"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1144 <param name="in" value="SRS014464-Anterior_nares-bowtie2out.tabular"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1145 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1146 <section name="mapping">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1147 <param name="bt2_ps" value="sensite"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1148 <param name="min_mapq_val" value="5"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1149 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1150 <section name="analysis">
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1151 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1152 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1153 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1154 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1155 <param name="split_levels" value="false"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1156 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1157 </conditional>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1158 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1159 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1160 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1161 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1162 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1163 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1164 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1165 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1166 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1167 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1168 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1169 <param name="legacy_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1170 <param name="CAMI_format_output" value="false"/>
10
289b3807e80c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit b8bc892a6d5eeae0b78c33058b532fcd52208179
iuc
parents: 8
diff changeset
1171 <param name="unclassified_estimation" value="false"/>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1172 <param name="krona_output" value="false"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1173 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1174 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1175 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1176 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1177 <has_text text="relative_abundance"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1178 <has_text text="NCBI_tax_id"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1179 <has_text text="clade_name"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1180 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1181 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1182 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1183 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1184 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1185 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1186 </output>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1187 <assert_stderr>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1188 <has_text text="Downloading" negate="true"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1189 </assert_stderr>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1190 </test>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1191 <!-- Single FASTA file, Cached db -->
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1192 <test expect_num_outputs="6">
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1193 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1194 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1195 <param name="selector" value="raw"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1196 <conditional name="raw_in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1197 <param name="selector" value="single"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1198 <param name="in" value="SRS014464-Anterior_nares.fasta"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1199 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1200 <param name="read_min_len" value="70"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1201 <section name="mapping">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1202 <param name="bt2_ps" value="sensitive"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1203 <param name="min_mapq_val" value="5"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1204 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1205 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1206 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1207 <param name="db_selector" value="cached"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1208 <param name="cached_db" value="test-db-20210409"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1209 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1210 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1211 <section name="analysis">
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1212 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1213 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1214 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1215 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1216 <param name="split_levels" value="true"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1217 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1218 </conditional>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1219 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1220 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1221 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1222 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1223 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1224 <param name="ignore_markers" value="marker.txt"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1225 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1226 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1227 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1228 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1229 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1230 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1231 <param name="legacy_output" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1232 <param name="CAMI_format_output" value="false"/>
10
289b3807e80c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit b8bc892a6d5eeae0b78c33058b532fcd52208179
iuc
parents: 8
diff changeset
1233 <param name="unclassified_estimation" value="false"/>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1234 <param name="krona_output" value="true"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1235 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1236 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1237 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1238 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1239 <has_text text="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1240 <has_text text="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1241 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1242 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1243 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-bowtie2out.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1244 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1245 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1246 <has_text text="37637__U2I1U8__N579_01580"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1247 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1248 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1249 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares.sam" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1250 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1251 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1252 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1253 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1254 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1255 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1256 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1257 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1258 </output>
12
1a037928504c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
iuc
parents: 11
diff changeset
1259 <output_collection name="levels" type="list">
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1260 <element name="all" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1261 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1262 <has_text text="Gammaproteobacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1263 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1264 <has_n_columns n="9"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1265 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1266 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1267 <element name="class" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1268 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1269 <has_text text="class"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1270 <has_text text="Actinobacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1271 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1272 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1273 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1274 <element name="family" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1275 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1276 <has_text text="family"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1277 <has_text text="Propionibacteriaceae"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1278 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1279 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1280 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1281 <element name="genus" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1282 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1283 <has_text text="genus"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1284 <has_text text="Cutibacterium"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1285 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1286 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1287 </element>
6
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1288 <element name="kingdom" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1289 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1290 <has_text text="kingdom"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1291 <has_text text="Bacteria"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1292 <has_n_columns n="2"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1293 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1294 </element>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1295 <element name="order" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1296 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1297 <has_text text="order"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1298 <has_text text="Propionibacteriales"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1299 <has_n_columns n="2"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1300 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1301 </element>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1302 <element name="phylum" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1303 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1304 <has_text text="phylum"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1305 <has_text text="Firmicutes"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1306 <has_n_columns n="2"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1307 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents: 5
diff changeset
1308 </element>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1309 <element name="species" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1310 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1311 <has_text text="species"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1312 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1313 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1314 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1315 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1316 <element name="strains" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1317 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1318 <has_text text="strains"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1319 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1320 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1321 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1322 </output_collection>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1323 <output name="krona_output_file" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1324 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1325 <not_has_text text="k__Bacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1326 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1327 <has_n_columns n="9"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1328 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1329 </output>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1330 <assert_stderr>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1331 <has_text text="Downloading" negate="true"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1332 </assert_stderr>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1333 </test>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1334 <!-- Check a non-default analysis mode
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1335 and viral analysis -->
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1336 <test expect_num_outputs="6">
8
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1337 <section name="inputs">
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1338 <conditional name="in">
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1339 <param name="selector" value="raw"/>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1340 <conditional name="raw_in">
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1341 <param name="selector" value="single"/>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1342 <param name="in" value="SRS014464-Anterior_nares.fastq.gz"/>
8
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1343 </conditional>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1344 </conditional>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1345 <conditional name="db">
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1346 <param name="db_selector" value="cached"/>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1347 <param name="cached_db" value="mpa_vJan21_TOY_CHOCOPhlAnSGB"/>
8
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1348 </conditional>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1349 </section>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1350 <section name="analysis">
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1351 <conditional name="analysis_type">
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1352 <param name="t" value="marker_ab_table"/>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1353 </conditional>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1354 </section>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1355 <conditional name="viral_analysis">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1356 <param name="profile_vsc" value="--profile_vsc"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1357 <param name="vsc_out" value="true"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1358 </conditional>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1359 <conditional name="subsample">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1360 <param name="selector" value="single"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1361 <param name="subsampling" value="10000"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1362 <param name="subsampling_seed" value="42"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1363 </conditional>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1364 <param name="test" value="true"/>
8
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1365 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size">
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1366 <assert_contents>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1367 <has_text text="SGB7017__MKDPKOFL_00679"/>
8
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1368 <has_text text="SampleID"/>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1369 <has_text text="Metaphlan_Analysis"/>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1370 </assert_contents>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents: 6
diff changeset
1371 </output>
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1372 <output name="subsample_single">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1373 <assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1374 <has_text text="@" n="10000"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1375 </assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1376 </output>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1377 <!-- reference data empty -> empty output -->
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1378 <output name="vcs_breath_coverage" ftype="tabular">
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1379 <assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1380 <has_size size="0"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1381 </assert_contents>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1382 </output>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1383 <assert_command>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1384 <has_text text="--profile_vsc"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1385 <has_text text="--vsc_breadth 0.75"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1386 <has_text text="--vsc_out"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1387 </assert_command>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1388 <assert_stderr>
12
1a037928504c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
iuc
parents: 11
diff changeset
1389 <has_text text="Downloading"/>
1a037928504c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
iuc
parents: 11
diff changeset
1390 <!-- due to test=true and the absence of the TOY reference DB Metaphlan will download to ~10MB-->
11
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents: 10
diff changeset
1391 <has_text text="No reads aligning to VSC markers"/>
b6897977d13e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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parents: 10
diff changeset
1392 </assert_stderr>
8
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iuc
parents: 6
diff changeset
1393 </test>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1394 </tests>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1395 <help><![CDATA[
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1396 What it does
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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parents:
diff changeset
1397 ============
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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parents:
diff changeset
1398
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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parents:
diff changeset
1399 MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria,
5
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parents: 3
diff changeset
1400 Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) at species-level.
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1401
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1402 MetaPhlAn relies on ~1.1M unique clade-specific marker genes identified from ~100,000 reference genomes
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1403 (~99,500 bacterial and archaeal and ~500 eukaryotic), allowing:
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1404
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1405 - unambiguous taxonomic assignments;
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1406 - accurate estimation of organismal relative abundance;
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1407 - species-level resolution for bacteria, archaea, eukaryotes and viruses;
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1408 - strain identification and tracking
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1409 - orders of magnitude speedups compared to existing methods.
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
1410 - microbiota strain-level population genomics
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1411
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1412 MetaPhlAn clade-abundance estimation
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1413 ------------------------------------
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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parents:
diff changeset
1414
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1415 The basic usage of MetaPhlAn consists in the identification of the clades (from phyla to species and
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
1416 strains in particular cases) present in the microbiota obtained from a microbiome sample and their
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1417 relative abundance.
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1418
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1419 Marker level analysis
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1420 ---------------------
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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parents:
diff changeset
1421
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1422 MetaPhlAn introduces the capability of characterizing organisms at the strain level using non
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1423 aggregated marker information. Such capability comes with several slightly different flavours and
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1424 are a way to perform strain tracking and comparison across multiple samples.
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1425
5
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
1426 Usually, MetaPhlAn is first ran with default parameters for the type of analysis to profile the
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
1427 species present in the community, and then a strain-level profiling can be performed to zoom-in on
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1428 specific species of interest. This operation can be performed quickly as it exploits the bowtie2out
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1429 intermediate file saved during the execution of the default analysis type.
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1430
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1431 Inputs
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1432 ======
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1433
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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diff changeset
1434 Metaphlan takes as input either:
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1435
5
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
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1436 - one or several sequence files in Fasta, FastQ (whether compressed or not)
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1437 - a BowTie2 produced SAM file
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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1438 - an intermediary mapping file of the microbiota generated by a previous MetaPhlAn run
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1439
5
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
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1440 It also needs the reference database, which can be locally installed or customized using the dedicated tools.
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1441
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1442 Outputs
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1443 =======
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1444
5
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
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1445 The main output is a tab-separated file with the predicted taxon relative abundances.
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1446
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1447 It also generates a BIOM file and some intermediate files (SAM and BowTie2out) if sequence files are given as inputs.
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1448
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1449
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1450 More help and use cases
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1451 =======================
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1452
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1453 To get more information about MetaPhlAn usage and use cases, please refer to the `Metaphlan documentation`_.
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1454
5
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
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1455 .. _Metaphlan documentation: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4#Basic-Usage
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1456
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1457 ]]></help>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1458 <expand macro="citations"/>
3
ff8f55893e7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit edceb1050e9e312ef8b1201cee35992720667b6a"
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1459 </tool>