Mercurial > repos > dfornika > micall_lite

annotate micall_lite.xml @ 29:4ff24c044fed draft default tip

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
author dfornika
date Thu, 27 Feb 2020 22:31:32 +0000
parents 966bfd22f6e5
children
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9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
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1 <tool id="micall_lite" name="micall_lite" version="@TOOL_VERSION@+galaxy0">
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2 <description></description>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">micall-lite</requirement>
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8 </requirements>
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9 <version_command>echo "@TOOL_VERSION@"</version_command>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
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12 #if str( $fastq_input.fastq_input_selector ) == "paired":
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13 #if $fastq_input.reads1.is_of_type("fastq.gz", "fastqsanger.gz"):
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14 #set unzipped = False
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15 #set reads1 = $fastq_input.reads1.name + '_R1.fastq.gz'
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16 #else if $fastq_input.reads1.is_of_type("fastq", "fastqsanger"):
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17 #set unzipped = True
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18 #set reads1 = $fastq_input.reads1.name + '_R1.fastq'
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19 #end if
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20 ln -s '$fastq_input.reads1' '$reads1' &&
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21 #if $fastq_input.reads2.is_of_type("fastq.gz", "fastqsanger.gz"):
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22 #set unzipped = False
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23 #set reads2 = $fastq_input.reads2.name + '_R2.fastq.gz'
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24 #else if $fastq_input.reads2.is_of_type("fastq", "fastqsanger"):
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25 #set unzipped = True
24
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26 #set reads2 = $fastq_input.reads2.name + '_R2.fastq'
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27 #end if
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
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28 ln -s '$fastq_input.reads2' '$reads2' &&
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29 #else if str( $fastq_input.fastq_input_selector ) == "paired_collection":
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
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30 #if $fastq_input.pair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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31 #set unzipped = False
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32 #set reads1 = $fastq_input.pair.name + '_R1.fastq.gz'
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33 #else if $fastq_input.pair.forward.is_of_type("fastq", "fastqsanger"):
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34 #set unzipped = True
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35 #set reads1 = $fastq_input.pair.name + '_R1.fastq'
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36 #end if
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
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37 ln -s '$fastq_input.pair.forward' '$reads1' &&
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38 #if $fastq_input.pair.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
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39 #set unzipped = False
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40 #set reads2 = $fastq_input.pair.name + '_R2.fastq.gz'
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41 #else if $fastq_input.pair.reverse.is_of_type("fastq", "fastqsanger"):
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42 #set unzipped = True
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43 #set reads2 = $fastq_input.pair.name + '_R2.fastq'
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44 #end if
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45 ln -s '$fastq_input.pair.reverse' '$reads2' &&
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46 #end if
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47
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
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48 mkdir 'outdir' &&
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49 micall
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50 --threads \${GALAXY_SLOTS:-1}
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51 --keep
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52 #if $unzipped:
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53 --unzipped
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54 #end if
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55 --readlen ${readlen}
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56 '${reads1}'
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57 '${reads2}'
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58 #if str( $projects_file_source.projects_file_source_selector ) == "tool_data_table":
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59 --projects '${projects_file_source.projects_file.fields.path}'
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60 #elif str( $projects_file_source.projects_file_source_selector ) == 'history':
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61 --projects '${projects_file_source.projects_file}'
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62 #end if
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63 --outdir 'outdir'
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64 ]]>
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65 </command>
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66 <inputs>
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67 <conditional name="fastq_input">
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68 <param name="fastq_input_selector" type="select" label="Paired Reads or Paired Collection" >
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69 <option selected="true" value="paired">Paired</option>
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70 <option value="paired_collection">Paired Collection</option>
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71 </param>
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72 <when value="paired">
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73 <param format="@INTYPES@" name="reads1" type="data" label="Select first set of reads"/>
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74 <param format="@INTYPES@" name="reads2" type="data" label="Select second set of reads"/>
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75 </when>
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76 <when value="paired_collection">
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
77 <param format="@INTYPES@" name="pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
78 </when>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
79 </conditional>
25
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
80 <conditional name="projects_file_source">
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
81 <param name="projects_file_source_selector" type="select"
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
82 label="Select a projects file from your history or use one from a tool data table?">
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
83 <option value="none" selected="true">No projects file</option>
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
84 <option value="tool_data_table">Projects file from tool data table</option>
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
85 <option value="history">Projects file from history</option>
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
86 </param>
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
87 <when value="none"/>
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
88 <when value="tool_data_table">
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
89 <param name="projects_file" type="select" format="json" label="MiCall-Lite Projects File">
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
90 <options from_data_table="micall_lite_projects_files">
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
91 <validator type="no_options" message="No MiCall-Lite projects files are available" />
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
92 </options>
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
93 </param>
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
94 </when>
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
95 <when value="history">
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
96 <param name="projects_file" type="data" format="json" label="MiCall-Lite Projects File" help=""/>
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
97 </when>
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
98 </conditional>
23
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
99 <param name="readlen" type="integer" min="1" value="251" max="600" label="Read Length" help="Read Length" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
100 </inputs>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
101 <outputs>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
102 <data name="align" label="align" format="csv" from_work_dir="outdir/*.align.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
103 <data name="amino" label="amino" format="csv" from_work_dir="outdir/*.amino.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
104 <data name="conseq" label="conseq" format="csv" from_work_dir="outdir/*.conseq.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
105 <data name="insert" label="insert" format="csv" from_work_dir="outdir/*.insert.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
106 <data name="nuc" label="nuc" format="csv" from_work_dir="outdir/*.nuc.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
107 </outputs>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
108 <tests>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
109 <test>
25
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
110 <conditional name="projects_file_source" >
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
111 <param name="projects_file_source_selector" value="none" />
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
112 </conditional>
23
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
113 <conditional name="fastq_input">
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
114 <param name="fastq_input_selector" value="paired"/>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
115 <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
116 <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
117 </conditional>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
118 <param name="readlen" value="51" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
119 <output name="align" value="1234A-V3LOOP.align.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
120 <output name="amino" value="1234A-V3LOOP.amino.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
121 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
122 <output name="insert" value="1234A-V3LOOP.insert.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
123 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
124 </test>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
125 <test>
25
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
126 <conditional name="projects_file_source" >
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
127 <param name="projects_file_source_selector" value="none" />
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
128 </conditional>
23
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
129 <conditional name="fastq_input">
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
130 <param name="fastq_input_selector" value="paired"/>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
131 <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
132 <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq.gz" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
133 </conditional>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
134 <param name="readlen" value="51" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
135 <output name="align" value="1234A-V3LOOP.align.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
136 <output name="amino" value="1234A-V3LOOP.amino.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
137 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
138 <output name="insert" value="1234A-V3LOOP.insert.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
139 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
140 </test>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
141 <test>
25
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
142 <conditional name="projects_file_source" >
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
143 <param name="projects_file_source_selector" value="none" />
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
144 </conditional>
23
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
145 <conditional name="fastq_input">
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
146 <param name="fastq_input_selector" value="paired_collection" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
147 <param name="pair" >
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
148 <collection type="paired">
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
149 <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
150 <element name="reverse" value="1234A-V3LOOP_S1_L001_R2_001.fastq" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
151 </collection>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
152 </param>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
parents:
diff changeset
153 </conditional>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
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154 <param name="readlen" value="51" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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155 <output name="align" value="1234A-V3LOOP.align.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
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156 <output name="amino" value="1234A-V3LOOP.amino.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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157 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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158 <output name="insert" value="1234A-V3LOOP.insert.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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159 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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160 </test>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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161 <test>
25
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
diff changeset
162 <conditional name="projects_file_source" >
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
parents: 24
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163 <param name="projects_file_source_selector" value="none" />
9ddbdfa79501 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 154f43d8bd11dc63d78a0504c4f985a42fa1267c-dirty"
dfornika
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diff changeset
164 </conditional>
23
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
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165 <conditional name="fastq_input">
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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166 <param name="fastq_input_selector" value="paired_collection" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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167 <param name="pair" >
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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168 <collection type="paired">
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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169 <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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170 <element name="reverse" value="1234A-V3LOOP_S1_L001_R2_001.fastq.gz" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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171 </collection>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
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172 </param>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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173 </conditional>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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174 <param name="readlen" value="51" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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175 <output name="align" value="1234A-V3LOOP.align.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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176 <output name="amino" value="1234A-V3LOOP.amino.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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177 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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178 <output name="insert" value="1234A-V3LOOP.insert.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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179 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
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180 </test>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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181 </tests>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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182 <help><![CDATA[
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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183 ]]></help>
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
dfornika
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184 <expand macro="citations" />
033e0a3674bc "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
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185 </tool>