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comparison mitos.xml @ 5:e03de7c5f99b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
author iuc
date Wed, 01 Mar 2023 22:39:06 +0000
parents 7ec1424f610d
children bfa34f944cf9
comparison
equal deleted inserted replaced
4:ceb5641ab502 5:e03de7c5f99b
1 <tool id="mitos" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> 1 <tool id="mitos" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>de-novo annotation of metazoan mitochondrial genomes</description> 2 <description>de-novo annotation of metazoan mitochondrial genomes</description>
3 <xrefs> 3 <xrefs>
4 <xref type='bio.tools'>mitos</xref> 4 <xref type='bio.tools'>mitos</xref>
5 </xrefs> 5 </xrefs>
6 <macros> 6 <macros>
7 <import>macros.xml</import> 7 <import>macros.xml</import>
8 <token name="@MITOS_NAME@">MITOS</token> 8 <token name="@MITOS_NAME@">MITOS</token>
9 <token name="@TOOL_VERSION@">1.0.5</token> 9 <token name="@TOOL_VERSION@">1.1.1</token>
10 <token name="@VERSION_SUFFIX@">1</token> 10 <token name="@VERSION_SUFFIX@">0</token>
11 </macros> 11 </macros>
12 <requirements> 12 <requirements>
13 <requirement type="package" version="@TOOL_VERSION@">mitos</requirement> 13 <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
14 <requirement type="package">zip</requirement>
15 </requirements> 14 </requirements>
16 <version_command>python -c "import mitos; print(mitos.__version__)"</version_command> 15 <version_command>python -c "import mitos; print(mitos.__version__)"</version_command>
17 <command detect_errors="aggressive"><![CDATA[ 16 <command detect_errors="aggressive"><![CDATA[
18 mkdir outdir && 17 mkdir outdir &&
19 18
35 --clipfac $advanced_prot.clipfac 34 --clipfac $advanced_prot.clipfac
36 #set fragovl=float($advanced_prot.fragovl)/100.0 35 #set fragovl=float($advanced_prot.fragovl)/100.0
37 --fragovl $fragovl 36 --fragovl $fragovl
38 --fragfac $advanced_prot.fragfac 37 --fragfac $advanced_prot.fragfac
39 --ststrange $advanced_prot.ststrange 38 --ststrange $advanced_prot.ststrange
40
41 #if "raw" in str($addoutputs).split(','): 39 #if "raw" in str($addoutputs).split(','):
42 && zip -9 -y -r output.zip outdir/ > /dev/null 40 --zip
43 #end if 41 #end if
44 ]]></command> 42 ]]></command>
45 <inputs> 43 <inputs>
46 <param argument="--input" label="sequence" type="data" format="fasta" help="a single sequence in fasta formated sequence"> 44 <param argument="--input" label="sequence" type="data" format="fasta" help="a single sequence in fasta formated sequence">
47 <options options_filter_attribute="metadata.sequences"> 45 <validator type="dataset_metadata_in_range" metadata_name="sequences" min="1" max="1"/>
48 <filter type="add_value" value="1"/>
49 </options>
50 </param> 46 </param>
51 <param argument="--code" label="Genetic code" type="select"> 47 <param argument="--code" label="Genetic code" type="select">
52 <option value="2">Vertebrate (2)</option> 48 <option value="2">Vertebrate (2)</option>
53 <option value="4">Mold, Protozoan, Coelenteral (4)</option> 49 <option value="4">Mold, Protozoan, Coelenteral (4)</option>
54 <option value="5">Invertebrate (5)</option> 50 <option value="5">Invertebrate (5)</option>
120 <filter>"protein_plot" in str(addoutputs)</filter> 116 <filter>"protein_plot" in str(addoutputs)</filter>
121 </data> 117 </data>
122 <data name="ncRNA_plot_out" format="pdf" from_work_dir="outdir/plots/rna.pdf" label="${tool.name} on ${on_string}: ncRNA prediction plot"> 118 <data name="ncRNA_plot_out" format="pdf" from_work_dir="outdir/plots/rna.pdf" label="${tool.name} on ${on_string}: ncRNA prediction plot">
123 <filter>"protein_plot" in str(addoutputs)</filter> 119 <filter>"protein_plot" in str(addoutputs)</filter>
124 </data> 120 </data>
125 <!--<collection name="ncRNA_structure_plot_ps_out" type="list" label="${tool.name} on ${on_string}: ncRNA postscript structure plots">
126 <discover_datasets pattern="(?P&lt;name&gt;.+)\.ps" format="ps" directory="outdir/plots" />
127 <filter>"ncRNA_structure_ps_plots" in str(addoutputs)</filter>
128 </collection>-->
129 <collection name="ncRNA_structure_plot_svg_out" type="list" label="${tool.name} on ${on_string}: ncRNA svg structure plots"> 121 <collection name="ncRNA_structure_plot_svg_out" type="list" label="${tool.name} on ${on_string}: ncRNA svg structure plots">
130 <discover_datasets pattern="(?P&lt;name&gt;.+)\.svg" format="svg" directory="outdir/plots" /> 122 <discover_datasets pattern="(?P&lt;name&gt;.+)\.svg" format="svg" directory="outdir/plots" />
131 <filter>"ncRNA_structure_svg_plots" in str(addoutputs)</filter> 123 <filter>"ncRNA_structure_svg_plots" in str(addoutputs)</filter>
132 </collection> 124 </collection>
133 <data name="rawout" format="zip" from_work_dir="output.zip" label="${tool.name} on ${on_string}: raw data"> 125 <data name="rawout" format="zip" from_work_dir="outdir.zip" label="${tool.name} on ${on_string}: raw data">
134 <filter>"raw" in str(addoutputs)</filter> 126 <filter>"raw" in str(addoutputs)</filter>
135 </data> 127 </data>
136 </outputs> 128 </outputs>
137 <tests> 129 <tests>
138 <!-- default options --> 130 <!-- default options -->
165 <output name="seqout" file="NC_012920.seq" ftype="txt" /> 157 <output name="seqout" file="NC_012920.seq" ftype="txt" />
166 <output name="fasout" file="NC_012920.fas" ftype="fasta" /> 158 <output name="fasout" file="NC_012920.fas" ftype="fasta" />
167 <output name="faaout" file="NC_012920.faa" ftype="fasta" /> 159 <output name="faaout" file="NC_012920.faa" ftype="fasta" />
168 <output name="rawout" ftype="zip"> 160 <output name="rawout" ftype="zip">
169 <assert_contents> 161 <assert_contents>
170 <has_archive_member path=".*/result.bed"/> 162 <has_archive_member path="result.bed"/>
171 </assert_contents> 163 </assert_contents>
172 </output> 164 </output>
173 <output name="geneorderout" file="NC_012920.geneorder" ftype="fasta" /> 165 <output name="geneorderout" file="NC_012920.geneorder" ftype="fasta" />
174 <output name="protein_plot_out" file="NC_012920_prot.pdf" ftype="pdf" compare="sim_size"/> 166 <output name="protein_plot_out" file="NC_012920_prot.pdf" ftype="pdf" compare="sim_size"/>
175 <output name="ncRNA_plot_out" file="NC_012920_ncrna.pdf" ftype="pdf" compare="sim_size"/> 167 <output name="ncRNA_plot_out" file="NC_012920_ncrna.pdf" ftype="pdf" compare="sim_size"/>