annotate micall_lite.xml @ 4:27d61a7f82f1 draft default tip

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit e58e1a02d64c2771fadf006bdf8f3661d069b6f3"
author public-health-bioinformatics
date Fri, 28 Feb 2020 13:03:00 -0500
parents 786c437c144c
children
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rev   line source
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e5390c4b69e9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
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1 <tool id="micall_lite" name="micall_lite" version="@TOOL_VERSION@+galaxy0">
3
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
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2 <description>
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
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3 Human RNA virus genotyping pipeline
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
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4 </description>
0
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">micall-lite</requirement>
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10 </requirements>
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11 <version_command>echo "@TOOL_VERSION@"</version_command>
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12 <command detect_errors="exit_code">
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13 <![CDATA[
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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14 #if str( $fastq_input.fastq_input_selector ) == "paired":
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15 #if $fastq_input.reads1.is_of_type("fastq.gz", "fastqsanger.gz"):
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16 #set unzipped = False
1
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17 #set reads1 = $fastq_input.reads1.name + '_R1.fastq.gz'
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18 #else if $fastq_input.reads1.is_of_type("fastq", "fastqsanger"):
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19 #set unzipped = True
1
bb549c5eaf34 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 5d661c102f12509d19c8869988c3f2f7ce00732b"
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20 #set reads1 = $fastq_input.reads1.name + '_R1.fastq'
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21 #end if
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22 ln -s '$fastq_input.reads1' '$reads1' &&
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23 #if $fastq_input.reads2.is_of_type("fastq.gz", "fastqsanger.gz"):
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24 #set unzipped = False
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25 #set reads2 = $fastq_input.reads2.name + '_R2.fastq.gz'
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26 #else if $fastq_input.reads2.is_of_type("fastq", "fastqsanger"):
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27 #set unzipped = True
1
bb549c5eaf34 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 5d661c102f12509d19c8869988c3f2f7ce00732b"
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28 #set reads2 = $fastq_input.reads2.name + '_R2.fastq'
0
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29 #end if
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30 ln -s '$fastq_input.reads2' '$reads2' &&
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31 #else if str( $fastq_input.fastq_input_selector ) == "paired_collection":
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32 #if $fastq_input.pair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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33 #set unzipped = False
1
bb549c5eaf34 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 5d661c102f12509d19c8869988c3f2f7ce00732b"
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34 #set reads1 = $fastq_input.pair.name + '_R1.fastq.gz'
0
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35 #else if $fastq_input.pair.forward.is_of_type("fastq", "fastqsanger"):
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36 #set unzipped = True
1
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37 #set reads1 = $fastq_input.pair.name + '_R1.fastq'
0
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38 #end if
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39 ln -s '$fastq_input.pair.forward' '$reads1' &&
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40 #if $fastq_input.pair.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
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41 #set unzipped = False
1
bb549c5eaf34 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 5d661c102f12509d19c8869988c3f2f7ce00732b"
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42 #set reads2 = $fastq_input.pair.name + '_R2.fastq.gz'
0
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43 #else if $fastq_input.pair.reverse.is_of_type("fastq", "fastqsanger"):
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44 #set unzipped = True
1
bb549c5eaf34 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 5d661c102f12509d19c8869988c3f2f7ce00732b"
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45 #set reads2 = $fastq_input.pair.name + '_R2.fastq'
0
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46 #end if
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47 ln -s '$fastq_input.pair.reverse' '$reads2' &&
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48 #end if
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49
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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50 mkdir 'outdir' &&
3
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51
0
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52 micall
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53 --threads \${GALAXY_SLOTS:-1}
3
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54 --keep
0
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55 #if $unzipped:
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56 --unzipped
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57 #end if
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58 --readlen ${readlen}
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59 '${reads1}'
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60 '${reads2}'
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61 #if str( $projects_file_source.projects_file_source_selector ) == "tool_data_table":
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62 --projects '${projects_file_source.projects_file.fields.path}'
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63 #elif str( $projects_file_source.projects_file_source_selector ) == 'history':
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64 --projects '${projects_file_source.projects_file}'
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65 #end if
0
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66 --outdir 'outdir'
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67 ]]>
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68 </command>
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69 <inputs>
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70 <conditional name="fastq_input">
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71 <param name="fastq_input_selector" type="select" label="Paired Reads or Paired Collection" >
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72 <option selected="true" value="paired">Paired</option>
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73 <option value="paired_collection">Paired Collection</option>
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74 </param>
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75 <when value="paired">
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76 <param format="@INTYPES@" name="reads1" type="data" label="Select first set of reads"/>
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diff changeset
77 <param format="@INTYPES@" name="reads2" type="data" label="Select second set of reads"/>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
78 </when>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
79 <when value="paired_collection">
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
80 <param format="@INTYPES@" name="pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
81 </when>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
82 </conditional>
3
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
83 <conditional name="projects_file_source">
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
84 <param name="projects_file_source_selector" type="select"
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
85 label="Select a projects file from your history or use one from a tool data table?">
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
86 <option value="none" selected="true">No projects file</option>
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
87 <option value="tool_data_table">Projects file from tool data table</option>
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
88 <option value="history">Projects file from history</option>
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
89 </param>
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
90 <when value="none"/>
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
91 <when value="tool_data_table">
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
92 <param name="projects_file" type="select" format="json" label="MiCall-Lite Projects File">
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
93 <options from_data_table="micall_lite_projects_files">
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
94 <validator type="no_options" message="No MiCall-Lite projects files are available" />
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
95 </options>
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
96 </param>
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
97 </when>
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
98 <when value="history">
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
99 <param name="projects_file" type="data" format="json" label="MiCall-Lite Projects File" help=""/>
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
100 </when>
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
101 </conditional>
0
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
102 <param name="readlen" type="integer" min="1" value="251" max="600" label="Read Length" help="Read Length" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
103 </inputs>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
104 <outputs>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
105 <data name="align" label="align" format="csv" from_work_dir="outdir/*.align.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
106 <data name="amino" label="amino" format="csv" from_work_dir="outdir/*.amino.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
107 <data name="conseq" label="conseq" format="csv" from_work_dir="outdir/*.conseq.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
108 <data name="insert" label="insert" format="csv" from_work_dir="outdir/*.insert.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
109 <data name="nuc" label="nuc" format="csv" from_work_dir="outdir/*.nuc.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
110 </outputs>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
111 <tests>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
112 <test>
3
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
113 <conditional name="projects_file_source" >
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
114 <param name="projects_file_source_selector" value="none" />
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
115 </conditional>
0
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
116 <conditional name="fastq_input">
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
117 <param name="fastq_input_selector" value="paired"/>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
118 <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
119 <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
120 </conditional>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
121 <param name="readlen" value="51" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
122 <output name="align" value="1234A-V3LOOP.align.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
123 <output name="amino" value="1234A-V3LOOP.amino.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
124 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
125 <output name="insert" value="1234A-V3LOOP.insert.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
126 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
127 </test>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
128 <test>
3
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
129 <conditional name="projects_file_source" >
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
130 <param name="projects_file_source_selector" value="none" />
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
131 </conditional>
0
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
132 <conditional name="fastq_input">
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
133 <param name="fastq_input_selector" value="paired"/>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
134 <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
135 <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq.gz" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
136 </conditional>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
137 <param name="readlen" value="51" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
138 <output name="align" value="1234A-V3LOOP.align.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
139 <output name="amino" value="1234A-V3LOOP.amino.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
140 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
141 <output name="insert" value="1234A-V3LOOP.insert.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
142 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
143 </test>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
144 <test>
3
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
145 <conditional name="projects_file_source" >
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
146 <param name="projects_file_source_selector" value="none" />
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
147 </conditional>
0
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
148 <conditional name="fastq_input">
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
149 <param name="fastq_input_selector" value="paired_collection" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
150 <param name="pair" >
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
151 <collection type="paired">
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
152 <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
153 <element name="reverse" value="1234A-V3LOOP_S1_L001_R2_001.fastq" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
154 </collection>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
155 </param>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
156 </conditional>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
157 <param name="readlen" value="51" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
158 <output name="align" value="1234A-V3LOOP.align.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
159 <output name="amino" value="1234A-V3LOOP.amino.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
160 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
161 <output name="insert" value="1234A-V3LOOP.insert.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
162 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
163 </test>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
164 <test>
3
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
165 <conditional name="projects_file_source" >
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
166 <param name="projects_file_source_selector" value="none" />
786c437c144c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
public-health-bioinformatics
parents: 2
diff changeset
167 </conditional>
0
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
168 <conditional name="fastq_input">
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
169 <param name="fastq_input_selector" value="paired_collection" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
170 <param name="pair" >
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
171 <collection type="paired">
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
172 <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
173 <element name="reverse" value="1234A-V3LOOP_S1_L001_R2_001.fastq.gz" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
174 </collection>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
175 </param>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
176 </conditional>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
177 <param name="readlen" value="51" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
178 <output name="align" value="1234A-V3LOOP.align.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
179 <output name="amino" value="1234A-V3LOOP.amino.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
180 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
181 <output name="insert" value="1234A-V3LOOP.insert.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
182 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
183 </test>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
184 </tests>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
185 <help><![CDATA[
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
186 ]]></help>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
187 <expand macro="citations" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
188 </tool>