Mercurial > repos > iuc > metaphlan
annotate metaphlan.xml @ 12:1a037928504c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
author | iuc |
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date | Sun, 11 Aug 2024 20:35:53 +0000 |
parents | b6897977d13e |
children | ef65b083bd0c |
rev | line source |
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12
1a037928504c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
iuc
parents:
11
diff
changeset
|
1 <tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
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
parents:
diff
changeset
|
3 <macros> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
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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changeset
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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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changeset
|
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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changeset
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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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changeset
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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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changeset
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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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changeset
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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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changeset
|
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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changeset
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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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changeset
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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
parents:
0
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changeset
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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
parents:
0
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changeset
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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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changeset
|
16 </param> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
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changeset
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17 <when value="a"> |
12
1a037928504c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
iuc
parents:
11
diff
changeset
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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
diff
changeset
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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
diff
changeset
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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
diff
changeset
|
21 <when value="p"/> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
22 <when value="c"/> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
23 <when value="o"/> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
24 <when value="f"/> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
25 <when value="g"/> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
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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> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
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29 <token name="@FILE_FORMATS@">fastq,fastq.gz,fastq.bz2,fasta,fasta.gz,fasta.bz2</token> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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30 </macros> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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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
parents:
diff
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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
parents:
diff
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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
parents:
diff
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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36 #if $inputs.in.raw_in.selector == "single" |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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37 #set full_ext=$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:
diff
changeset
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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
parents:
diff
changeset
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39 #set $file_path="in" |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
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40 zcat '$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
parents:
diff
changeset
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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
parents:
diff
changeset
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42 #set $file_path="in" |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
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43 bzcat '$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
parents:
diff
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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
parents:
diff
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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
parents:
diff
changeset
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47 #else if $inputs.in.raw_in.selector == "multiple" |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
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48 #set full_ext=$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
parents:
diff
changeset
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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
parents:
diff
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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
parents:
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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
parents:
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52 #if $f.datatype.file_ext != $full_ext |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
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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
parents:
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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
parents:
diff
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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
parents:
diff
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56 #if $full_ext.endswith("gz") |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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57 #set fp="input_%s" % ($i) |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
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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
parents:
diff
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59 #else if $full_ext.endswith("bz2") |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
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60 #set fp="input_%s" % ($i) |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
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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
parents:
diff
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62 #else |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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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
parents:
diff
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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
parents:
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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
parents:
diff
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66 #set $sep="," |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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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
parents:
diff
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68 #else if $inputs.in.raw_in.selector == "paired" |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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69 #set full_ext=$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
parents:
diff
changeset
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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
diff
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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
parents:
10
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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
parents:
diff
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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:
diff
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74 #if $full_ext.endswith("gz") |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
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75 zcat '$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
diff
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76 zcat '$inputs.in.raw_in.in_r' > 'in_r' && |
b6897977d13e
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77 #set file_path="-1 in_f -2 in_r" |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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78 #else if $full_ext.endswith("bz2") |
11
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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79 bzcat '$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
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80 bzcat '$inputs.in.raw_in.in_r' > 'in_r' && |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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81 #set file_path="-1 in_f -2 in_r" |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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82 #else |
11
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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83 #set file_path="-1 '%s' -2 '%s'" % ($inputs.in.raw_in.in_f,$inputs.in.raw_in.in_r) |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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84 #end if |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
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85 #else if $inputs.in.raw_in.selector == "paired_collection" |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
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86 #set full_ext=$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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87 #if $full_ext != $inputs.in.raw_in.in.reverse.ext |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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88 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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89 exit 1 |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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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 #if $full_ext.endswith("gz") |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
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92 zcat '$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
iuc
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93 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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94 #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
iuc
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95 #else if $full_ext.endswith("bz2") |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
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96 bzcat '$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
iuc
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97 bzcat '$inputs.in.raw_in.in.reverse' > 'in_r' && |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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98 #set file_path="-1 in_f -2 in_r" |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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99 #else |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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100 #set file_path="-1 '%s' -2 '%s'" % ($inputs.in.raw_in.in_f,$inputs.in.raw_in.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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101 #end if |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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102 #end if |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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103 |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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104 #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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105 #set ext='fastq' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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106 #else if $full_ext.startswith("fasta") and $full_ext.endswith(("gz","bz2")) |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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107 #set ext='fasta' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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108 #else |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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109 #set ext=$full_ext |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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110 #end if |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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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 |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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113 #if $inputs.db.db_selector == "history" |
11
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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114 mkdir 'ref_db' && |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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115 bowtie2-build --large-index '$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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116 python |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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117 '$__tool_directory__/customizemetadata.py' |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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118 transform_json_to_pkl |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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119 --json '$inputs.db.mpa_pkl' |
11
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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120 --pkl 'ref_db/custom_db.pkl' && |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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121 #end if |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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122 |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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123 metaphlan |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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124 #if $inputs.in.selector == "raw" |
11
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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125 $file_path |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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126 --input_type '$ext' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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127 --read_min_len $inputs.in.read_min_len |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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128 --bt2_ps '$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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129 --min_mapq_val $inputs.in.mapping.min_mapq_val |
5
6dee4abadccb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
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130 #if $ext == "sam" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
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131 --nreads \$(cat '$file_path' | grep -c -v '^@') |
6dee4abadccb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
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132 #end if |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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133 #else |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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134 '$inputs.in.in' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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135 --input_type '$inputs.in.selector' |
5
6dee4abadccb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
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136 #if $inputs.in.selector == "sam" |
6dee4abadccb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
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137 --nreads \$(cat '$inputs.in.in' | grep -c -v '^@') |
6dee4abadccb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
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138 #end if |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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139 #end if |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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140 #if $inputs.db.db_selector == "cached" |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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141 --bowtie2db '$inputs.db.cached_db.fields.path' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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142 --index '$inputs.db.cached_db.fields.dbkey' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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143 #else |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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144 --bowtie2db 'ref_db/' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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145 --index 'custom_db' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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146 #end if |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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147 -t '$analysis.analysis_type.t' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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148 #if $analysis.analysis_type.t == "rel_ab" or $analysis.analysis_type.t == "rel_ab_w_read_stats" |
1
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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0
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149 --tax_lev '$analysis.analysis_type.tax_lev.tax_lev' |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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150 #else if $analysis.analysis_type.t == "clade_specific_strain_tracker" |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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151 --clade '$analysis.analysis_type.clade' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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152 #if str($analysis.analysis_type.min_ab) != '' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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|
153 --min_ab $analysis.analysis_type.min_ab |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
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154 #end if |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
155 #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"
iuc
parents:
diff
changeset
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156 --nreads $$analysis.analysis_type.nreads |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
157 #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
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158 --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
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159 #end if |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
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160 --min_cu_len $analysis.min_cu_len |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
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161 #if str($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
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162 --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
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163 #end if |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
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164 #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
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165 --add_viruses |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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166 #end if |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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167 #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
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168 --ignore_eukaryotes |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
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169 #end if |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
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170 #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
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171 --ignore_bacteria |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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172 #end if |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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173 #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
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174 --ignore_archaea |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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175 #end if |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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176 --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
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177 --perc_nonzero $analysis.perc_nonzero |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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178 #if $analysis.ignore_markers |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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179 --ignore_markers '$analysis.ignore_markers' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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180 #end if |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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181 $analysis.avoid_disqm |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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182 --sample_id_key '$out.sample_id_key' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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183 --sample_id '$out.sample_id' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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184 $out.use_group_representative |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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185 $out.legacy_output |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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186 $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
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187 $out.unclassified_estimation |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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188 -o '$output_file' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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189 --bowtie2out 'bowtie2out' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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190 -s '$sam_output_file' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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191 --biom '$biom_output_file' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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|
192 --nproc \${GALAXY_SLOTS:-4} |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
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193 #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
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194 $viral_analysis.profile_vsc |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
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195 --vsc_out '$vcs_breath_coverage' |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
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196 --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
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197 #end if |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
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198 |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
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199 #if $subsample.selector != "no" |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
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200 #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
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201 --subsampling $subsample.subsampling |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
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202 #else |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
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203 --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
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204 #end if |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
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205 $subsample.mapping_subsampling |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
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206 #if $subsample.subsampling_seed |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
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207 --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
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208 #end if |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
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209 --subsampling_output subsampled.out |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
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210 #end if |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
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211 |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
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212 #if $test == "false" |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
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213 --offline |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
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214 #end if |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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215 |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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216 #if $inputs.in.selector == "raw" |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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217 && |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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218 mv 'bowtie2out' '$bowtie2out' |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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219 #end if |
1
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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0
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|
220 |
2
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
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221 |
8
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents:
6
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222 #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:
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223 #if $analysis.analysis_type.tax_lev.tax_lev == 'a' and $analysis.analysis_type.tax_lev.split_levels |
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents:
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224 && |
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents:
6
diff
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|
225 mkdir 'split_levels' |
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents:
6
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226 && |
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents:
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227 python '$__tool_directory__/formatoutput.py' |
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
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228 split_levels |
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents:
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229 --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
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230 --outdir 'split_levels' |
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents:
6
diff
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231 $out.legacy_output |
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents:
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diff
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232 #end if |
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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|
233 #end if |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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0
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234 |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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0
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235 #if $out.krona_output |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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0
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|
236 && |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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237 python '$__tool_directory__/formatoutput.py' |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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238 format_for_krona |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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239 --metaphlan_output '$output_file' |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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240 --krona_output '$krona_output_file' |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
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241 #end if |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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242 ]]></command> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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243 <inputs> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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244 <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
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245 <conditional name="in"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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246 <param name="selector" type="select" label="Input(s)"> |
2
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
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247 <option value="raw" selected="true">Fasta/FastQ file(s) with microbiota reads</option> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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248 <option value="sam">Externally BowTie2-mapped SAM file</option> |
2
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
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249 <option value="bowtie2out">Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run</option> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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250 </param> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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251 <when value="raw"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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252 <conditional name="raw_in"> |
2
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
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253 <param name="selector" type="select" label="Fasta/FastQ file(s) with microbiota reads"> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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254 <option value="single" selected="true">One single-end file</option> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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255 <option value="multiple">Multiple single-end files</option> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
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256 <option value="paired_collection">Paired-end collection</option> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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257 <option value="paired">Paired-end files</option> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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258 </param> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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259 <when value="single"> |
2
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
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260 <param name="in" type="data" format="@FILE_FORMATS@" label="Single-end Fasta/FastQ file with microbiota reads"/> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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261 </when> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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262 <when value="multiple"> |
12
1a037928504c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
iuc
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diff
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263 <param name="in" type="data" format="@FILE_FORMATS@" label="Single-end Fasta/FastQ files with microbiota reads" multiple="true"/> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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264 </when> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
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265 <when value="paired_collection"> |
12
1a037928504c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
iuc
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266 <param name="in" type="data_collection" format="@FILE_FORMATS@" label="Paired-end Fasta/FastQ file with microbiota reads" collection_type="paired"/> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
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267 </when> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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268 <when value="paired"> |
2
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
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269 <param name="in_f" type="data" format="@FILE_FORMATS@" label="Forward paired-end Fasta/FastQ file with microbiota reads"/> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
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270 <param name="in_r" type="data" format="@FILE_FORMATS@" label="Reverse paired-end Fasta/FastQ file with microbiota reads"/> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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271 </when> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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272 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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273 <param argument="--read_min_len" type="integer" value="70" label="Minimum length of the reads to be considered when parsing the input file"/> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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274 <section name="mapping" title="Mapping" expanded="true"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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275 <param argument="--bt2_ps" type="select" label="Presets options for BowTie2" help="Applied only with FASTA files"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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276 <option value="sensitive">Sensitive</option> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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277 <option value="very-sensitive" selected="true">Very sensitive</option> |
3
ff8f55893e7d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit edceb1050e9e312ef8b1201cee35992720667b6a"
iuc
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|
278 <option value="sensitive-local">Sensitive local</option> |
ff8f55893e7d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit edceb1050e9e312ef8b1201cee35992720667b6a"
iuc
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279 <option value="very-sensitive-local">Very sensitive local</option> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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280 </param> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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281 <param argument="--min_mapq_val" type="integer" value="5" label="Minimum mapping quality value (MAPQ)"/> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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282 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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283 </when> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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284 <when value="sam"> |
2
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
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1
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|
285 <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
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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286 </when> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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287 <when value="bowtie2out"> |
12
1a037928504c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
iuc
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288 <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 >3.0"/> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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289 </when> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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290 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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291 <conditional name="db"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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292 <param name="db_selector" type="select" label="Database with clade-specific marker genes"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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293 <option value="cached" selected="true">Locally cached</option> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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294 <option value="history">From history</option> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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295 </param> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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296 <when value="cached"> |
6
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
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297 <param name="cached_db" type="select" label="Cached database with clade-specific marker genes"> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
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298 <options from_data_table="@IDX_DATA_TABLE@"> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
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299 <filter type="static_value" column="4" value="@IDX_VERSION@"/> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
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300 <validator message="No compatible MetaPhlAn database is available" type="no_options"/> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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301 </options> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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302 </param> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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303 </when> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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304 <when value="history"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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|
305 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/> |
6
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
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diff
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306 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associated to the database with clade-specific marker genes from history"/> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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307 </when> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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308 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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309 </section> |
f5df500fcc3c
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310 <section name="analysis" title="Analysis" expanded="true"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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311 <conditional name="analysis_type"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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312 <param argument="-t" type="select" label="Type of analysis to perform"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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313 <option value="rel_ab" selected="true">rel_ab: Profiling a microbiota in terms of relative abundances</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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314 <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> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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315 <option value="reads_map">reads_map: Mapping from reads to clades (only reads hitting a marker)</option> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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316 <option value="clade_profiles">clade_profiles: Normalized marker counts for clades with at least a non-null marker</option> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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317 <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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318 <option value="marker_ab_table">marker_ab_table: Normalized marker counts (only when > 0.0 and normalized by microbiota size if number of reads is specified)</option> |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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319 <option value="marker_counts">marker_counts: Non-normalized marker counts (use with extreme caution)</option> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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320 <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> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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321 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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322 <when value="rel_ab"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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323 <expand macro="tax_lev"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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324 </when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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325 <when value="rel_ab_w_read_stats"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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326 <expand macro="tax_lev"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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327 </when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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328 <when value="reads_map"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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329 <when value="clade_profiles"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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330 <when value="clade_specific_strain_tracker"> |
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331 <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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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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332 <param argument="--min_ab" type="float" optional="true" label="The minimum percentage abundance for the clade"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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333 </when> |
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334 <when value="marker_ab_table"> |
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335 <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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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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336 </when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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337 <when value="marker_counts"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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338 <when value="marker_pres_table"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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339 <param argument="--pres_th" type="integer" optional="true" label="Threshold for calling a marker present"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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340 </when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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341 </conditional> |
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342 <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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343 <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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344 <param name="organism_profiling" type="select" optional="true" label="Organisms to profile" multiple="true"> |
0
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345 <option value="add_viruses" selected="true">Profile viral organisms (add_viruses)</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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346 <option value="ignore_eukaryotes">Ignore eukaryotic organisms (ignore_eukaryotes)</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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347 <option value="ignore_bacteria">Ignore bacteria organisms (ignore_bacteria)</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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348 <option value="ignore_archaea">Ignore archea organisms (ignore_archaea)</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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349 </param> |
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350 <param argument="--stat" type="select" label="Statistical approach for converting marker abundances into clade abundances"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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351 <option value="avg_g">avg_g: Clade global (i.e. normalizing all markers together) average (avg_g)</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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352 <option value="avg_l">avg_l: Average of length-normalized marker counts</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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353 <option value="tavg_g" selected="true">tavg_g: Truncated clade global average at --stat_q quantile</option> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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354 <option value="tavg_l">tavg_l: Truncated average of length-normalized marker counts (at --stat_q)</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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355 <option value="wavg_g">wavg_g: Winsorized clade global average (at --stat_q)</option> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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356 <option value="wavg_l">wavg_l: Winsorized average of length-normalized marker counts (at --stat_q)</option> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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357 <option value="med">med: Median of length-normalized marker counts</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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358 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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359 <param argument="--stat_q" type="float" value="0.2" label="Quantile value for the robust average"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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360 <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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361 <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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362 <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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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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363 </section> |
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364 <conditional name="subsample"> |
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365 <param name="selector" type="select" label="Subsample" help="Subsampling only works for fastq input"> |
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366 <option value="no">No</option> |
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367 <option value="single">Yes: specify number of reads</option> |
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368 <option value="paired">Yes: specify number of paired reads</option> |
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369 </param> |
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370 <when value="no"/> |
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371 <when value="single"> |
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372 <param argument="--subsampling" type="integer" min="1" value="" label="Sumbsample reads" help="Specify the number of reads to be considered"/> |
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373 <expand macro="subsample_common"/> |
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374 </when> |
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375 <when value="paired"> |
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376 <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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377 <expand macro="subsample_common"/> |
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378 </when> |
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379 </conditional> |
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380 <conditional name="viral_analysis"> |
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381 <param argument="--profile_vsc" type="select" label="Profile Viruses with VSCs approach"> |
b6897977d13e
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382 <option value="--profile_vsc">Yes (requires FASTQ input and reference data with VSG fasta)</option> |
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383 <option value="" selected="true">No</option> |
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384 </param> |
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385 <when value="--profile_vsc"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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386 <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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387 </when> |
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388 <when value=""/> |
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389 </conditional> |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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390 <section name="out" title="Outputs" expanded="true"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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391 <param argument="--sample_id_key" type="text" value="SampleID" label="Sample ID key for this analysis"/> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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392 <param argument="--sample_id" type="text" value="Metaphlan_Analysis" label="Sample ID for this analysis"/> |
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393 <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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394 <param argument="--legacy-output" type="boolean" truevalue="--legacy-output" falsevalue="" checked="false" label="Old MetaPhlAn2 two columns output?"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
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395 <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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396 <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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
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397 <param name="krona_output" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output for Krona?"/> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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398 </section> |
11
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399 <!-- enabling this in tests will allow metaphlan to download reference data (we do this only with the smallish TOY DB) --> |
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400 <param name="test" type="hidden" value="false"/> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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401 </inputs> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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402 <outputs> |
12
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403 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances"/> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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404 <data name="bowtie2out" format="tabular" label="${tool.name} on ${on_string}: Bowtie2 output"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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405 <filter>inputs['in']['selector'] == "raw"</filter> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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406 </data> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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407 <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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408 <filter>inputs['in']['selector'] == "raw"</filter> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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409 </data> |
12
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410 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
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411 <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels"> |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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412 <discover_datasets pattern="(?P<designation>.+)" directory="split_levels/" format="tabular"/> |
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413 <filter>analysis['analysis_type']['t'] in ['rel_ab', 'rel_ab_w_read_stats'] and analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter> |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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414 </collection> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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415 <data name="krona_output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances for Krona"> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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416 <filter>out['krona_output']</filter> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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417 </data> |
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418 <data name="vcs_breath_coverage" format="tabular" label="${tool.name} on ${on_string}: VSCs breadth-of-coverage"> |
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419 <filter>viral_analysis['profile_vsc']</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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420 </data> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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421 <data name="subsample_single" format="fastqsanger" from_work_dir="subsampled.out" label="${tool.name} on ${on_string}: Subsampled reads"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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422 <filter>subsample['selector'] == 'single'</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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423 </data> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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424 <collection name="subsample_paired" type="paired" label="${tool.name} on ${on_string}: Subsampled paired reads"> |
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425 <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
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426 <data name="reverse" format="fastqsanger" from_work_dir="subsampled.R2.out"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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427 <filter>subsample['selector'] == 'paired'</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
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428 </collection> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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429 </outputs> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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430 <tests> |
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431 <!-- Single GZ file, Cached db --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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432 <test expect_num_outputs="6"> |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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433 <section name="inputs"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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434 <conditional name="in"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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435 <param name="selector" value="raw"/> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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436 <conditional name="raw_in"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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437 <param name="selector" value="single"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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438 <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"
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439 </conditional> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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440 <param name="read_min_len" value="70"/> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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441 <section name="mapping"> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
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442 <param name="bt2_ps" value="sensitive"/> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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443 <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
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444 </section> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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445 </conditional> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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446 <conditional name="db"> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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447 <param name="db_selector" value="cached"/> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
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448 <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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449 </conditional> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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450 </section> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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451 <section name="analysis"> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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452 <conditional name="analysis_type"> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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453 <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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|
454 <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
|
455 <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
|
456 <param name="split_levels" value="true"/> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
457 </conditional> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
458 </conditional> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
459 <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
|
460 <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
|
461 <param name="stat" value="avg_g"/> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
462 <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
|
463 <param name="perc_nonzero" value="0.33"/> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
464 <param name="avoid_disqm" value="true"/> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
465 </section> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
466 <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
|
467 <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
|
468 <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
|
469 <param name="use_group_representative" value="false"/> |
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="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
|
471 <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
|
472 <param name="unclassified_estimation" value="false"/> |
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="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
|
474 </section> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
475 <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
|
476 <assert_contents> |
5
6dee4abadccb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents:
3
diff
changeset
|
477 <has_text text="UNCLASSIFIED"/> |
2
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
478 </assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
479 </output> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
480 <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
|
481 <assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
482 <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
|
483 <has_n_lines n="2"/> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
484 </assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
485 </output> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
486 <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
|
487 <assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
488 <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
|
489 </assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
490 </output> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
491 <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
|
492 <assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
493 <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
|
494 <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
|
495 </assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
496 </output> |
8
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents:
6
diff
changeset
|
497 <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
|
498 <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
|
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 <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
|
501 <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
|
502 <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
|
503 </assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
504 </element> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
505 <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
|
506 <assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
507 <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
|
508 <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
|
509 <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
|
510 <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
|
511 </assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
512 </element> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
513 <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
|
514 <assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
515 <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
|
516 <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
|
517 <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
|
518 <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
|
519 </assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
520 </element> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
521 <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
|
522 <assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
523 <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
|
524 <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
|
525 <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
|
526 <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
|
527 </assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
528 </element> |
6
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
529 <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
|
530 <assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
531 <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
|
532 <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
|
533 <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
|
534 </assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
535 </element> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
536 <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
|
537 <assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
538 <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
|
539 <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
|
540 <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
|
541 <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
|
542 </assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
543 </element> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
544 <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
|
545 <assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
546 <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
|
547 <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
|
548 <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
|
549 <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
|
550 </assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
551 </element> |
2
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
552 <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
|
553 <assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
554 <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
|
555 <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
|
556 <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
|
557 <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
|
558 </assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
559 </element> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
560 <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
|
561 <assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
562 <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
|
563 <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
|
564 <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
|
565 <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
|
566 </assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
567 </element> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
568 </output_collection> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
569 <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
|
570 <assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
571 <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
|
572 <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
|
573 <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
|
574 </assert_contents> |
a92a632c4d9b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents:
1
diff
changeset
|
575 </output> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
576 <assert_stderr> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
577 <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
|
578 </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
|
579 </test> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
580 <!-- 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
|
581 <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
|
582 <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
|
583 <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
|
584 <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
|
585 <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
|
586 <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
|
587 <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
|
588 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
589 <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
|
590 <section name="mapping"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
591 <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
|
592 <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
|
593 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
594 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
595 <conditional name="db"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
596 <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
|
597 <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
|
598 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
599 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
600 <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
|
601 <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
|
602 <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
|
603 <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
|
604 <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
|
605 <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
|
606 </conditional> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
607 </conditional> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
608 <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
|
609 <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
|
610 <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
|
611 <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
|
612 <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
|
613 <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
|
614 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
615 <section name="out"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
616 <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
|
617 <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
|
618 <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
|
619 <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
|
620 <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
|
621 <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
|
622 <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
|
623 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
624 <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
|
625 <assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
626 <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
|
627 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
628 </output> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
629 <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
|
630 <assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
631 <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
|
632 <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
|
633 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
634 </output> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
635 <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
|
636 <assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
637 <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
|
638 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
639 </output> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
640 <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
|
641 <assert_contents> |
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="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
|
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> |
12
1a037928504c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
iuc
parents:
11
diff
changeset
|
645 <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
|
646 <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
|
647 <assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
648 <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
|
649 <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
|
650 <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
|
651 </assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
652 </element> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
653 <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
|
654 <assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
655 <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
|
656 <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
|
657 <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
|
658 <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
|
659 </assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
660 </element> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
661 <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
|
662 <assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
663 <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
|
664 <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
|
665 <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
|
666 <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
|
667 </assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
668 </element> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
669 <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
|
670 <assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
671 <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
|
672 <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
|
673 <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
|
674 <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
|
675 </assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
676 </element> |
6
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
677 <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
|
678 <assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
679 <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
|
680 <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
|
681 <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
|
682 </assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
683 </element> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
684 <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
|
685 <assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
686 <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
|
687 <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
|
688 <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
|
689 <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
|
690 </assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
691 </element> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
692 <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
|
693 <assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
694 <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
|
695 <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
|
696 <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
|
697 <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
|
698 </assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
699 </element> |
1
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
700 <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
|
701 <assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
702 <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
|
703 <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
|
704 <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
|
705 <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
|
706 </assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
707 </element> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
708 <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
|
709 <assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
710 <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
|
711 <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
|
712 <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
|
713 </assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
714 </element> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
715 </output_collection> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
716 <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
|
717 <assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
718 <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
|
719 <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
|
720 <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
|
721 </assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
722 </output> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
723 <assert_stderr> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
724 <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
|
725 </assert_stderr> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
726 </test> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
727 <!-- 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
|
728 <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
|
729 <section name="inputs"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
730 <conditional name="in"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
731 <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
|
732 <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
|
733 <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
|
734 <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
|
735 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
736 <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
|
737 <section name="mapping"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
738 <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
|
739 <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
|
740 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
741 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
742 <conditional name="db"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
743 <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
|
744 <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
|
745 <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
|
746 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
747 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
748 <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
|
749 <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
|
750 <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
|
751 <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
|
752 <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
|
753 <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
|
754 </conditional> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
755 </conditional> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
756 <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
|
757 <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
|
758 <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
|
759 <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
|
760 <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
|
761 <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
|
762 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
763 <section name="out"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
764 <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
|
765 <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
|
766 <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
|
767 <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
|
768 <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
|
769 <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
|
770 <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
|
771 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
772 <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
|
773 <assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
774 <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
|
775 <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
|
776 <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
|
777 <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
|
778 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
779 </output> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
780 <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
|
781 <assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
782 <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
|
783 <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
|
784 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
785 </output> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
786 <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
|
787 <assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
788 <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
|
789 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
790 </output> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
791 <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
|
792 <assert_contents> |
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="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
|
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> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
796 <assert_stderr> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
797 <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
|
798 </assert_stderr> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
799 </test> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
800 <!-- 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
|
801 <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
|
802 <section name="inputs"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
803 <conditional name="in"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
804 <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
|
805 <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
|
806 <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
|
807 <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
|
808 <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
|
809 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
810 <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
|
811 <section name="mapping"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
812 <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
|
813 <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
|
814 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
815 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
816 <conditional name="db"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
817 <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
|
818 <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
|
819 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
820 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
821 <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
|
822 <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
|
823 <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
|
824 <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
|
825 <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
|
826 <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
|
827 </conditional> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
828 </conditional> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
829 <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
|
830 <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
|
831 <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
|
832 <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
|
833 <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
|
834 <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
|
835 </section> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
836 <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
|
837 <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
|
838 <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
|
839 <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
|
840 </conditional> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
841 <section name="out"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
842 <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
|
843 <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
|
844 <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
|
845 <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
|
846 <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
|
847 <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
|
848 <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
|
849 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
850 <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
|
851 <assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
852 <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
|
853 <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
|
854 <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
|
855 <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
|
856 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
857 </output> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
858 <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
|
859 <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
|
860 <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
|
861 <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
|
862 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
863 </output> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
864 <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
|
865 <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
|
866 <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
|
867 <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
|
868 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
869 </output> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
870 <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
|
871 <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
|
872 <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
|
873 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
874 </output> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
875 <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
|
876 <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
|
877 <assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
878 <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
|
879 </assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
880 </element> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
881 <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
|
882 <assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
883 <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
|
884 </assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
885 </element> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
886 </output_collection> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
887 <assert_stderr> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
888 <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
|
889 </assert_stderr> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
890 </test> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
891 <!-- 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
|
892 <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
|
893 <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
|
894 <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
|
895 <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
|
896 <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
|
897 <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
|
898 <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
|
899 <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
|
900 <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
|
901 <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
|
902 </collection> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
903 </param> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
904 </conditional> |
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="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
|
906 <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
|
907 <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
|
908 <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
|
909 </section> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
910 </conditional> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
911 <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
|
912 <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
|
913 <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
|
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 </section> |
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="analysis"> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
917 <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
|
918 <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
|
919 <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
|
920 <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
|
921 <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
|
922 </conditional> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
923 </conditional> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
924 <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
|
925 <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
|
926 <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
|
927 <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
|
928 <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
|
929 <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
|
930 </section> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
931 <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
|
932 <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
|
933 <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
|
934 <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
|
935 </conditional> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
936 <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
|
937 <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
|
938 <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
|
939 <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
|
940 <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
|
941 <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
|
942 <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
|
943 <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
|
944 </section> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
945 <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
|
946 <assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
947 <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
|
948 <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
|
949 <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
|
950 <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
|
951 </assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
952 </output> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
953 <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
|
954 <assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
955 <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
|
956 <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
|
957 </assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
958 </output> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
959 <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
|
960 <assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
961 <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
|
962 <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
|
963 </assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
964 </output> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
965 <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
|
966 <assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
967 <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
|
968 </assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
969 </output> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
970 <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
|
971 <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
|
972 <assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
973 <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
|
974 </assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
975 </element> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
976 <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
|
977 <assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
978 <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
|
979 </assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
980 </element> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
981 </output_collection> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
982 <assert_stderr> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
983 <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
|
984 </assert_stderr> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
985 </test> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
986 <!-- 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
|
987 <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
|
988 <section name="inputs"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
989 <conditional name="in"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
990 <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
|
991 <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
|
992 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
993 <conditional name="db"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
994 <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
|
995 <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
|
996 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
997 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
998 <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
|
999 <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
|
1000 <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
|
1001 <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
|
1002 <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
|
1003 <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
|
1004 </conditional> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1005 </conditional> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1006 <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
|
1007 <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
|
1008 <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
|
1009 <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
|
1010 <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
|
1011 <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
|
1012 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1013 <section name="out"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1014 <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
|
1015 <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
|
1016 <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
|
1017 <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
|
1018 <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
|
1019 <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
|
1020 <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
|
1021 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1022 <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
|
1023 <assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1024 <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
|
1025 <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
|
1026 <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
|
1027 <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
|
1028 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1029 </output> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1030 <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
|
1031 <assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1032 <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
|
1033 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1034 </output> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1035 <assert_stderr> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1036 <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
|
1037 </assert_stderr> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1038 </test> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1039 <!-- 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
|
1040 <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
|
1041 <section name="inputs"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1042 <conditional name="in"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1043 <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
|
1044 <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
|
1045 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1046 <conditional name="db"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1047 <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
|
1048 <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
|
1049 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1050 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1051 <conditional name="in"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1052 <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
|
1053 <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
|
1054 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1055 <section name="mapping"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1056 <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
|
1057 <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
|
1058 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1059 <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
|
1060 <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
|
1061 <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
|
1062 <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
|
1063 <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
|
1064 <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
|
1065 </conditional> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1066 </conditional> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1067 <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
|
1068 <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
|
1069 <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
|
1070 <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
|
1071 <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
|
1072 <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
|
1073 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1074 <section name="out"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1075 <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
|
1076 <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
|
1077 <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
|
1078 <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
|
1079 <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
|
1080 <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
|
1081 <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
|
1082 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1083 <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
|
1084 <assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1085 <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
|
1086 <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
|
1087 <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
|
1088 <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
|
1089 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1090 </output> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1091 <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
|
1092 <assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1093 <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
|
1094 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1095 </output> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1096 <assert_stderr> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1097 <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
|
1098 </assert_stderr> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1099 </test> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1100 <!-- 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
|
1101 <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
|
1102 <section name="inputs"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1103 <conditional name="in"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1104 <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
|
1105 <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
|
1106 <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
|
1107 <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
|
1108 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1109 <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
|
1110 <section name="mapping"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1111 <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
|
1112 <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
|
1113 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1114 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1115 <conditional name="db"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1116 <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
|
1117 <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
|
1118 </conditional> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1119 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1120 <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
|
1121 <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
|
1122 <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
|
1123 <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
|
1124 <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
|
1125 <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
|
1126 </conditional> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1127 </conditional> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1128 <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
|
1129 <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
|
1130 <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
|
1131 <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
|
1132 <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
|
1133 <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
|
1134 <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
|
1135 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1136 <section name="out"> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1137 <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
|
1138 <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
|
1139 <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
|
1140 <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
|
1141 <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
|
1142 <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
|
1143 <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
|
1144 </section> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1145 <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
|
1146 <assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1147 <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
|
1148 <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
|
1149 <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
|
1150 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1151 </output> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1152 <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
|
1153 <assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1154 <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
|
1155 <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
|
1156 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1157 </output> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1158 <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
|
1159 <assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1160 <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
|
1161 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1162 </output> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1163 <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
|
1164 <assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1165 <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
|
1166 </assert_contents> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1167 </output> |
12
1a037928504c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb
iuc
parents:
11
diff
changeset
|
1168 <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
|
1169 <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
|
1170 <assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1171 <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
|
1172 <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
|
1173 <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
|
1174 </assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1175 </element> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1176 <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
|
1177 <assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1178 <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
|
1179 <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
|
1180 <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
|
1181 </assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1182 </element> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1183 <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
|
1184 <assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1185 <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
|
1186 <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
|
1187 <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
|
1188 </assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1189 </element> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1190 <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
|
1191 <assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1192 <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
|
1193 <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
|
1194 <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
|
1195 </assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1196 </element> |
6
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
1197 <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
|
1198 <assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
1199 <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
|
1200 <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
|
1201 <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
|
1202 </assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
1203 </element> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
1204 <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
|
1205 <assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
1206 <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
|
1207 <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
|
1208 <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
|
1209 </assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
1210 </element> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
1211 <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
|
1212 <assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
1213 <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
|
1214 <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
|
1215 <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
|
1216 </assert_contents> |
2131d7dca455
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
iuc
parents:
5
diff
changeset
|
1217 </element> |
1
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1218 <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
|
1219 <assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1220 <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
|
1221 <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
|
1222 <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
|
1223 </assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1224 </element> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1225 <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
|
1226 <assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1227 <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
|
1228 <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
|
1229 </assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1230 </element> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1231 </output_collection> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1232 <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
|
1233 <assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1234 <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
|
1235 <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
|
1236 <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
|
1237 </assert_contents> |
b89b0765695d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents:
0
diff
changeset
|
1238 </output> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1239 <assert_stderr> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1240 <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
|
1241 </assert_stderr> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1242 </test> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1243 <!-- 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
|
1244 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
|
1245 <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
|
1246 <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
|
1247 <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
|
1248 <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
|
1249 <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
|
1250 <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
|
1251 <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
|
1252 </conditional> |
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents:
6
diff
changeset
|
1253 </conditional> |
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents:
6
diff
changeset
|
1254 <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
|
1255 <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
|
1256 <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
|
1257 </conditional> |
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents:
6
diff
changeset
|
1258 </section> |
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents:
6
diff
changeset
|
1259 <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
|
1260 <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
|
1261 <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
|
1262 </conditional> |
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents:
6
diff
changeset
|
1263 </section> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1264 <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
|
1265 <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
|
1266 <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
|
1267 </conditional> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1268 <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
|
1269 <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
|
1270 <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
|
1271 <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
|
1272 </conditional> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1273 <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
|
1274 <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
|
1275 <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
|
1276 <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
|
1277 <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
|
1278 <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
|
1279 </assert_contents> |
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents:
6
diff
changeset
|
1280 </output> |
11
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1281 <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
|
1282 <assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1283 <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
|
1284 </assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1285 </output> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1286 <!-- 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
|
1287 <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
|
1288 <assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1289 <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
|
1290 </assert_contents> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1291 </output> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1292 <assert_command> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1293 <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
|
1294 <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
|
1295 <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
|
1296 </assert_command> |
b6897977d13e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
iuc
parents:
10
diff
changeset
|
1297 <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
|
1298 <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
|
1299 <!-- 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
|
1300 <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
iuc
parents:
10
diff
changeset
|
1301 </assert_stderr> |
8
1a6cdf55390f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
iuc
parents:
6
diff
changeset
|
1302 </test> |
0
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1303 </tests> |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1304 <help><![CDATA[ |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1305 What it does |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1306 ============ |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
1307 |
f5df500fcc3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
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|
1308 MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, |
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1309 Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) at species-level. |
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1310 |
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1311 MetaPhlAn relies on ~1.1M unique clade-specific marker genes identified from ~100,000 reference genomes |
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1312 (~99,500 bacterial and archaeal and ~500 eukaryotic), allowing: |
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1313 |
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1314 - unambiguous taxonomic assignments; |
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1315 - accurate estimation of organismal relative abundance; |
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1316 - species-level resolution for bacteria, archaea, eukaryotes and viruses; |
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1317 - strain identification and tracking |
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1318 - orders of magnitude speedups compared to existing methods. |
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1319 - microbiota strain-level population genomics |
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1320 |
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1321 MetaPhlAn clade-abundance estimation |
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1322 ------------------------------------ |
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1323 |
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1324 The basic usage of MetaPhlAn consists in the identification of the clades (from phyla to species and |
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1325 strains in particular cases) present in the microbiota obtained from a microbiome sample and their |
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1326 relative abundance. |
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1327 |
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1328 Marker level analysis |
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1329 --------------------- |
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1330 |
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1331 MetaPhlAn introduces the capability of characterizing organisms at the strain level using non |
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1332 aggregated marker information. Such capability comes with several slightly different flavours and |
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1333 are a way to perform strain tracking and comparison across multiple samples. |
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1334 |
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1335 Usually, MetaPhlAn is first ran with default parameters for the type of analysis to profile the |
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1336 species present in the community, and then a strain-level profiling can be performed to zoom-in on |
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1337 specific species of interest. This operation can be performed quickly as it exploits the bowtie2out |
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1338 intermediate file saved during the execution of the default analysis type. |
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1339 |
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1340 Inputs |
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1341 ====== |
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1342 |
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1343 Metaphlan takes as input either: |
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1344 |
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1345 - one or several sequence files in Fasta, FastQ (whether compressed or not) |
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1346 - a BowTie2 produced SAM file |
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1347 - an intermediary mapping file of the microbiota generated by a previous MetaPhlAn run |
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1348 |
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1349 It also needs the reference database, which can be locally installed or customized using the dedicated tools. |
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1350 |
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1351 Outputs |
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1352 ======= |
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1353 |
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1354 The main output is a tab-separated file with the predicted taxon relative abundances. |
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1355 |
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1356 It also generates a BIOM file and some intermediate files (SAM and BowTie2out) if sequence files are given as inputs. |
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1357 |
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1358 |
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1359 More help and use cases |
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1360 ======================= |
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1361 |
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1362 To get more information about MetaPhlAn usage and use cases, please refer to the `Metaphlan documentation`_. |
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1363 |
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1364 .. _Metaphlan documentation: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4#Basic-Usage |
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1365 |
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1366 ]]></help> |
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1367 <expand macro="citations"/> |
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1368 </tool> |