Mercurial > repos > iuc > fargene

annotate fargene.xml @ 1:239ce9f24386 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 0b2de0d35b6ef4c0ef0dd77e8415115a4a3b415b"
author iuc
date Mon, 02 Dec 2019 04:39:18 -0500
parents 6f743c615c41
children b982a9ea939c
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1
239ce9f24386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 0b2de0d35b6ef4c0ef0dd77e8415115a4a3b415b"
iuc
parents: 0
diff changeset
1 <tool id="fargene" name="fargene" version="@VERSION@+galaxy1">
0
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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2 <description>Fragmented antibiotic resistance gene identifier </description>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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3 <macros>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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4 <import>macros.xml</import>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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5 </macros>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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6 <expand macro="requirements" />
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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7 <version_command>fargene --version</version_command>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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8 <command detect_errors="exit_code"><![CDATA[
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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9 #import re
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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10 #if $inputs.input_type == 'paired':
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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11 #set $safename_R1 = re.sub('[^\w\-_\.]', '_', $inputs.R1.element_identifier)
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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12 #set $safename_R2 = re.sub('[^\w\-_\.]', '_', $inputs.R2.element_identifier)
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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13 ln -fs '$inputs.R1' ${safename_R1}.fastq &&
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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14 ln -fs '$inputs.R2' ${safename_R2}.fastq &&
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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15 #elif $inputs.input_type == 'collection':
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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16 #for $i, $input in enumerate($inputs.input_collection)
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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17 #set $safename_fwd = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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18 ln -fs '${input.forward}' ${safename_fwd}_1.fastq &&
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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19 #set $safename_rvs = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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20 ln -fs '${input.reverse}' ${safename_rvs}_2.fastq &&
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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21 #end for
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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22 #elif $inputs.input_type == 'sequence':
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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23 #for $input in $inputs.input_sequence
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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24 #set $safename_seq = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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25 ln -fs '$input' ${safename_seq}.fasta &&
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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26 #end for
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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27 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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28
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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29 fargene
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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30 --infiles
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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31 #if $inputs.input_type in ('paired', 'collection'):
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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32 *.fastq
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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33 --meta
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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34 #elif $inputs.input_type == 'sequence':
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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35 *.fasta
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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36 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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37 --hmm-model $models
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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38 --output fargene_output
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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39 --tmp-dir tmp
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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40 -p \${GALAXY_SLOTS:-4}
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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41 #if $meta_score != 0.0:
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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42 --meta-score '$meta_score'
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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43 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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44 #if $score != 0.0:
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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45 --score '$score'
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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46 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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47 #if $protein:
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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48 '$protein'
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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49 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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50 #if $min_orf_length != 90:
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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51 --min-orf-length '$min_orf_length'
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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52 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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53 #if $retrieve_whole:
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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54 '$retrieve_whole'
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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55 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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56 #if $no_orf_predict:
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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57 '$no_orf_predict'
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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58 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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59 #if $no_quality_filtering:
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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60 '$no_quality_filtering'
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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61 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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62 #if $no_assembly:
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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63 '$no_assembly'
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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64 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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65 #if $orf_finder:
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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66 '$orf_finder'
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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67 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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68 #if $store_peptides:
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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69 '$store_peptides'
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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70 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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71 &&
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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72 #if $inputs.input_type in ('paired', 'collection'):
1
239ce9f24386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 0b2de0d35b6ef4c0ef0dd77e8415115a4a3b415b"
iuc
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73 tar -czf retrievedFragments.tar.gz fargene_output/retrievedFragments
0
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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74 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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75 2>&1
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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76 ]]> </command>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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77 <inputs>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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78 <conditional name="inputs">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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79 <param name="input_type" type="select" label="Input type" help="Select 'paired end' reads or 'sequence' for genomes/contigs">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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80 <option value="paired" selected="true">Paired</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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81 <option value="collection">Paired Collection</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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82 <option value="sequence">Contigs/Genomes</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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83 </param>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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84 <when value="paired">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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85 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
86 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
87 </when>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
88 <when value="collection">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
89 <param name="input_collection" format="fastqsanger" type="data_collection" collection_type="list:paired" label="Paired collection"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
90 </when>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
91 <when value="sequence">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
92 <param name="input_sequence" type="data" format="fasta" multiple="true" label="Input contigs/genomes" />
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
93 </when>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
94 </conditional>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
95
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
96 <param name="models" type="select" label="Resistance Genes">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
97 <option value="class_a">Class A beta-lactamases</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
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98 <option value="class_b_1_2">Subclass B1 and B2 beta-lactamases</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
99 <option value="class_b_3">Subclass B3 beta-lactamases</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
100 <option value="class_c">Class C beta-lactamases</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
101 <option value="class_d_1">Class D beta-lactamases-1</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
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102 <option value="class_d_2">Class D beta-lactamases-2</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
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103 <option value="qnr">QNR</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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parents:
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104 </param>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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parents:
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105 <param name="score" argument="--score" type="float" value="0.0" label="The threshold score for a sequence to be classified as
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
106 a (almost) complete gene" />
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
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107 <param name="meta_score" argument="--meta-score" type="float" value="0.0" label="The threshold score for a fragment to be classified as
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
108 a positive. Expressed as score per amino acid" />
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
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109 <param name="protein" argument="--protein" type="boolean" truevalue="--protein" falsevalue="" checked="False" label="Rescue short unassmebled plasmids" />
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
110 <param name="min_orf_length" argument="--min-orf-length" type="integer" min="1" value="90" label="The minimal length for a retrieved predicted ORF (nt)" />
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
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111 <param name="retrieve_whole" argument="--retrieve-whole" type="boolean" truevalue="--retrieve-whole " falsevalue="" checked="False" label="Use this flag if the whole sequence where a hit is
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
112 detected should be retrieved" />
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
113 <param name="no_orf_predict" argument="--no-orf-predict" type="boolean" truevalue="--no-orf-predict" falsevalue="" checked="False" label="Do not perform ORF prediction" />
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
114 <param name="no_quality_filtering" argument="--no-quality-filtering" type="boolean" truevalue="--no-quality-filtering" falsevalue="" checked="False" label="Use if no quality control should be performed on the
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
115 metagenomic data" />
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
116 <param name="no_assembly" argument="--no-assembly" type="boolean" truevalue="--no-assembly" falsevalue="" checked="False" label="Use if you want to skip the assembly and retrieval of
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
117 contigs for metagenomic data" />
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
118 <param name="orf_finder" argument="--orf-finder" type="boolean" truevalue="--orf-finder" falsevalue="" checked="False" label="Use NCBI ORFfinder instead of prodigal for ORF
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
119 prediction of genomes/contigs" />
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
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120 <param name="store_peptides" argument="--store-peptides" type="boolean" truevalue="--store-peptides" falsevalue="" checked="False" label="Store the translated sequences. Useful if you plan to
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
121 redo the analysis using a different model and want to
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
122 skip the preprocessing steps" />
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
123
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
124 </inputs>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
125 <outputs>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
126 <data name="summary" format="txt" from_work_dir="fargene_output/results_summary.txt" label="${tool.name} on ${on_string} (Summary)">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
127 </data>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
128 <data name="retrievedFragments" format="tar.gz" from_work_dir="retrievedFragments.tar.gz" label="${tool.name} on ${on_string} (Retrieved Fragments)">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
129 <filter>inputs["input_type"] in ['paired' , 'collection']</filter>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
130 </data>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
131 <data name="fargene_log" format="txt" from_work_dir="fargene_analysis.log" label="${tool.name} on ${on_string} (log)">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
132 </data>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
133 <collection name="hmmsearchresults" type="list" label="HMM Search Result">
1
239ce9f24386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 0b2de0d35b6ef4c0ef0dd77e8415115a4a3b415b"
iuc
parents: 0
diff changeset
134 <discover_datasets pattern="(?P&lt;name&gt;.+).out" directory="fargene_output/hmmsearchresults" format="txt" visible="false" />
0
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
135 </collection>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
136 <collection name="predictedGenes" type="list" label="Predicted Genes">
1
239ce9f24386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 0b2de0d35b6ef4c0ef0dd77e8415115a4a3b415b"
iuc
parents: 0
diff changeset
137 <discover_datasets pattern="(?P&lt;name&gt;.+).fasta" directory="fargene_output/predictedGenes" format="fasta" visible="false" />
0
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
138 </collection>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
139 </outputs>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
140 <tests>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
141 <test expect_num_outputs="5">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
142 <conditional name="inputs">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
143 <param name="input_type" value="paired"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
144 <param name="R1" value="reads_1.fastq"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
145 <param name="R2" value="reads_2.fastq"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
146 </conditional>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
147 <output name="summary" file="paired/results_summary.txt" compare="sim_size"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
148 </test>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
149 <test expect_num_outputs="5">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
150 <conditional name="inputs">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
151 <param name="input_type" value="collection"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
152 <param name="input_collection">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
153 <collection type="list:paired">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
154 <element name="Pair1">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
155 <collection type="paired">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
156 <element name="forward" value="reads_1.fastq" ftype="fastqsanger"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
157 <element name="reverse" value="reads_2.fastq" ftype="fastqsanger"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
158 </collection>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
159 </element>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
160 </collection>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
161 </param>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
162 </conditional>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
163 <output name="summary" file="paired/results_summary.txt" compare="sim_size"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
164 </test>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
165 <test expect_num_outputs="4">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
diff changeset
166 <conditional name="inputs">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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167 <param name="input_type" value="sequence"/>
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168 <param name="input_sequence" value="klebsiella_plasmid.fasta"/>
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169 <param name="models" value="class_b_1_2" />
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170 </conditional>
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171 <output name="summary" file="contigs/results_summary.txt" compare="sim_size"/>
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172 </test>
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173 </tests>
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174 <help><![CDATA[
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175
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176 fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. The tool includes developed and optimized models for a number or resistance gene types, and the functionality to create and optimize models of your own choice of resistance genes.
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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177
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178 The current version of the tool includes developed and optimized models for identification of the following resistance genes
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179
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180 - Class A beta-lactamases
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181 - Subclass B1 and B2 beta-lactamases
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182 - Subclass B3 beta-lactamases
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183 - Class C beta-lactamases
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184 - Class D beta-lactamases
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185 - qnr
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186 ]]>
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187 </help>
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188 <expand macro="citations" />
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189 </tool>