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comparison micall_lite.xml @ 3:786c437c144c draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 2436110003f0cf659a4f7e7d5b7312e8b84ad9db"
author public-health-bioinformatics
date Thu, 27 Feb 2020 19:15:39 -0500
parents e5390c4b69e9
children
comparison
equal deleted inserted replaced
2:e5390c4b69e9 3:786c437c144c
1 <tool id="micall_lite" name="micall_lite" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="micall_lite" name="micall_lite" version="@TOOL_VERSION@+galaxy0">
2 <description></description> 2 <description>
3 Human RNA virus genotyping pipeline
4 </description>
3 <macros> 5 <macros>
4 <import>macros.xml</import> 6 <import>macros.xml</import>
5 </macros> 7 </macros>
6 <requirements> 8 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">micall-lite</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">micall-lite</requirement>
44 #end if 46 #end if
45 ln -s '$fastq_input.pair.reverse' '$reads2' && 47 ln -s '$fastq_input.pair.reverse' '$reads2' &&
46 #end if 48 #end if
47 49
48 mkdir 'outdir' && 50 mkdir 'outdir' &&
51
49 micall 52 micall
50 --threads \${GALAXY_SLOTS:-1} 53 --threads \${GALAXY_SLOTS:-1}
54 --keep
51 #if $unzipped: 55 #if $unzipped:
52 --unzipped 56 --unzipped
53 #end if 57 #end if
54 --readlen ${readlen} 58 --readlen ${readlen}
55 '${reads1}' 59 '${reads1}'
56 '${reads2}' 60 '${reads2}'
61 #if str( $projects_file_source.projects_file_source_selector ) == "tool_data_table":
62 --projects '${projects_file_source.projects_file.fields.path}'
63 #elif str( $projects_file_source.projects_file_source_selector ) == 'history':
64 --projects '${projects_file_source.projects_file}'
65 #end if
57 --outdir 'outdir' 66 --outdir 'outdir'
58 ]]> 67 ]]>
59 </command> 68 </command>
60 <inputs> 69 <inputs>
61 <conditional name="fastq_input"> 70 <conditional name="fastq_input">
69 </when> 78 </when>
70 <when value="paired_collection"> 79 <when value="paired_collection">
71 <param format="@INTYPES@" name="pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/> 80 <param format="@INTYPES@" name="pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/>
72 </when> 81 </when>
73 </conditional> 82 </conditional>
83 <conditional name="projects_file_source">
84 <param name="projects_file_source_selector" type="select"
85 label="Select a projects file from your history or use one from a tool data table?">
86 <option value="none" selected="true">No projects file</option>
87 <option value="tool_data_table">Projects file from tool data table</option>
88 <option value="history">Projects file from history</option>
89 </param>
90 <when value="none"/>
91 <when value="tool_data_table">
92 <param name="projects_file" type="select" format="json" label="MiCall-Lite Projects File">
93 <options from_data_table="micall_lite_projects_files">
94 <validator type="no_options" message="No MiCall-Lite projects files are available" />
95 </options>
96 </param>
97 </when>
98 <when value="history">
99 <param name="projects_file" type="data" format="json" label="MiCall-Lite Projects File" help=""/>
100 </when>
101 </conditional>
74 <param name="readlen" type="integer" min="1" value="251" max="600" label="Read Length" help="Read Length" /> 102 <param name="readlen" type="integer" min="1" value="251" max="600" label="Read Length" help="Read Length" />
75 </inputs> 103 </inputs>
76 <outputs> 104 <outputs>
77 <data name="align" label="align" format="csv" from_work_dir="outdir/*.align.csv" /> 105 <data name="align" label="align" format="csv" from_work_dir="outdir/*.align.csv" />
78 <data name="amino" label="amino" format="csv" from_work_dir="outdir/*.amino.csv" /> 106 <data name="amino" label="amino" format="csv" from_work_dir="outdir/*.amino.csv" />
80 <data name="insert" label="insert" format="csv" from_work_dir="outdir/*.insert.csv" /> 108 <data name="insert" label="insert" format="csv" from_work_dir="outdir/*.insert.csv" />
81 <data name="nuc" label="nuc" format="csv" from_work_dir="outdir/*.nuc.csv" /> 109 <data name="nuc" label="nuc" format="csv" from_work_dir="outdir/*.nuc.csv" />
82 </outputs> 110 </outputs>
83 <tests> 111 <tests>
84 <test> 112 <test>
113 <conditional name="projects_file_source" >
114 <param name="projects_file_source_selector" value="none" />
115 </conditional>
85 <conditional name="fastq_input"> 116 <conditional name="fastq_input">
86 <param name="fastq_input_selector" value="paired"/> 117 <param name="fastq_input_selector" value="paired"/>
87 <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq" /> 118 <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq" />
88 <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq" /> 119 <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq" />
89 </conditional> 120 </conditional>
93 <output name="conseq" value="1234A-V3LOOP.conseq.csv" /> 124 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
94 <output name="insert" value="1234A-V3LOOP.insert.csv" /> 125 <output name="insert" value="1234A-V3LOOP.insert.csv" />
95 <output name="nuc" value="1234A-V3LOOP.nuc.csv" /> 126 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
96 </test> 127 </test>
97 <test> 128 <test>
129 <conditional name="projects_file_source" >
130 <param name="projects_file_source_selector" value="none" />
131 </conditional>
98 <conditional name="fastq_input"> 132 <conditional name="fastq_input">
99 <param name="fastq_input_selector" value="paired"/> 133 <param name="fastq_input_selector" value="paired"/>
100 <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" /> 134 <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" />
101 <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq.gz" /> 135 <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq.gz" />
102 </conditional> 136 </conditional>
106 <output name="conseq" value="1234A-V3LOOP.conseq.csv" /> 140 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
107 <output name="insert" value="1234A-V3LOOP.insert.csv" /> 141 <output name="insert" value="1234A-V3LOOP.insert.csv" />
108 <output name="nuc" value="1234A-V3LOOP.nuc.csv" /> 142 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
109 </test> 143 </test>
110 <test> 144 <test>
145 <conditional name="projects_file_source" >
146 <param name="projects_file_source_selector" value="none" />
147 </conditional>
111 <conditional name="fastq_input"> 148 <conditional name="fastq_input">
112 <param name="fastq_input_selector" value="paired_collection" /> 149 <param name="fastq_input_selector" value="paired_collection" />
113 <param name="pair" > 150 <param name="pair" >
114 <collection type="paired"> 151 <collection type="paired">
115 <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq" /> 152 <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq" />
123 <output name="conseq" value="1234A-V3LOOP.conseq.csv" /> 160 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
124 <output name="insert" value="1234A-V3LOOP.insert.csv" /> 161 <output name="insert" value="1234A-V3LOOP.insert.csv" />
125 <output name="nuc" value="1234A-V3LOOP.nuc.csv" /> 162 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
126 </test> 163 </test>
127 <test> 164 <test>
165 <conditional name="projects_file_source" >
166 <param name="projects_file_source_selector" value="none" />
167 </conditional>
128 <conditional name="fastq_input"> 168 <conditional name="fastq_input">
129 <param name="fastq_input_selector" value="paired_collection" /> 169 <param name="fastq_input_selector" value="paired_collection" />
130 <param name="pair" > 170 <param name="pair" >
131 <collection type="paired"> 171 <collection type="paired">
132 <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" /> 172 <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" />