Mercurial > repos > iuc > orthofinder_onlygroups

comparison orthofinder_only_groups.xml @ 1:918d141a166b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
author iuc
date Sun, 03 Dec 2017 04:30:59 -0500
parents bfb20dbe1309
children 649b98adce77
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0:bfb20dbe1309 1:918d141a166b
1 <tool name="OrthoFinder OnlyGroups" id="orthofinder_onlygroups" version="1.1.4"> 1 <tool name="OrthoFinder OnlyGroups" id="orthofinder_onlygroups" version="1.1.4">
2 <description>finds orthogroups in a set of proteomes</description> 2 <description>finds orthogroups in a set of proteomes</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.4">orthofinder</requirement> 4 <requirement type="package" version="1.1.4">orthofinder</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 <![CDATA[ 7 <![CDATA[
8 ## prepare inputs 8 ## prepare inputs
9 #if $init.start=="fasta": 9 #if $init.start=="fasta":
10 #set $infiles = "" 10 #set $infiles = ""
11 #for $input in $init.input_fasta 11 #for $input in $init.input_fasta
12 ln -s '$input' '$input.element_identifier' && 12 ln -s '$input' '${input.element_identifier}.fasta' &&
13 #set $infiles = $infiles + str($input.element_identifier) + "," 13 #set $infiles = $infiles + str($input.element_identifier) + ","
14 #end for 14 #end for
15 #set $infiles = $infiles[:-1] 15 #set $infiles = $infiles[:-1]
16 #elif $init.start=="blast": 16 #elif $init.start=="blast":
17 #set $infilesbl = "" 17 #set $infilesbl = ""
104 <data format="txt" name="SequenceIDs" label="SequencesIDs.txt" from_work_dir="results/WorkingDirectory/SequenceIDs.txt" > 104 <data format="txt" name="SequenceIDs" label="SequencesIDs.txt" from_work_dir="results/WorkingDirectory/SequenceIDs.txt" >
105 <filter>init['start']=="fasta" and init['keepblastout']</filter> 105 <filter>init['start']=="fasta" and init['keepblastout']</filter>
106 </data> 106 </data>
107 </outputs> 107 </outputs>
108 <tests> 108 <tests>
109 <!-- test orthofinder -f . -og when input files has no extension fasta/faa/fa ... -->
110 <test>
111 <conditional name="init">
112 <param name="start" value="fasta" />
113 <param name="input_fasta" ftype="fasta" value="inputs/no_fa_ext/AcAcaud_trinity,inputs/no_fa_ext/AmAmphi_trinity,inputs/no_fa_ext/ApApomp_trinity,inputs/no_fa_ext/AsAsp1_trinity" />
114 <param name="keepblastout" value="no" />
115 </conditional>
116 <param name="inflation" value="1.5" />
117 <output name="specs_overlap">
118 <assert_contents>
119 <has_text text="AcAcaud_trinity"/>
120 <has_text text="AmAmphi_trinity"/>
121 <has_text text="ApApomp_trinity"/>
122 <has_text text="AsAsp1_trinity"/>
123 <has_n_columns n="5"/>
124 </assert_contents>
125 </output>
126 <output name="unassigned_genes">
127 <assert_contents>
128 <has_text text="AcAcaud_trinity"/>
129 <has_text text="AmAmphi_trinity"/>
130 <has_text text="ApApomp_trinity"/>
131 <has_text text="AsAsp1_trinity"/>
132 <has_n_columns n="5"/>
133 </assert_contents>
134 </output>
135 <output name="stat_overall">
136 <assert_contents>
137 <has_text text="Number of genes in orthogroups"/>
138 <has_text text="Number of unassigned genes"/>
139 <has_text text="Percentage of orthogroups"/>
140 <has_text text="Number of orthogroups"/>
141 <has_text text="Number of genes"/>
142 <has_text text="G50 (assigned genes)"/>
143 <has_text text="G50 (all genes)"/>
144 <has_text text="O50 (assigned genes)"/>
145 <has_text text="O50 (all genes)"/>
146 </assert_contents>
147 </output>
148 <output name="stat_specs">
149 <assert_contents>
150 <has_text text="AcAcaud_trinity"/>
151 <has_text text="AmAmphi_trinity"/>
152 <has_text text="ApApomp_trinity"/>
153 <has_text text="AsAsp1_trinity"/>
154 <has_text text="Number of genes per-species in orthogroup"/>
155 <has_text text="Percentage of orthogroups"/>
156 <has_text text="Number of orthogroups"/>
157 <has_text text="Number of genes"/>
158 <has_n_columns n="5"/>
159 </assert_contents>
160 </output>
161 </test>
109 <!-- test orthofinder -f -og --> 162 <!-- test orthofinder -f -og -->
110 <test> 163 <test>
111 <conditional name="init"> 164 <conditional name="init">
112 <param name="start" value="fasta" /> 165 <param name="start" value="fasta" />
113 <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" /> 166 <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />
209 <has_text text="Number of orthogroups"/> 262 <has_text text="Number of orthogroups"/>
210 <has_text text="Number of genes"/> 263 <has_text text="Number of genes"/>
211 <has_n_columns n="5"/> 264 <has_n_columns n="5"/>
212 </assert_contents> 265 </assert_contents>
213 </output> 266 </output>
214 <output name="SpeciesIDs" value="inputs/blastids/SpeciesIDs.txt" />
215 <output name="SequenceIDs" value="inputs/blastids/SequenceIDs.txt" /> 267 <output name="SequenceIDs" value="inputs/blastids/SequenceIDs.txt" />
216 <output_collection name="wdfasta" type="list" count="4"/> 268 <output_collection name="wdfasta" type="list" count="4"/>
217 <output_collection name="wdblast" type="list" count="16"/> 269 <output_collection name="wdblast" type="list" count="16"/>
218 </test> 270 </test>
219 271
258 <output name="specs_overlap" value="results_fromblast/Orthogroups_SpeciesOverlaps.csv"/> 310 <output name="specs_overlap" value="results_fromblast/Orthogroups_SpeciesOverlaps.csv"/>
259 <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.csv"/> 311 <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.csv"/>
260 <output name="stat_overall" value="results_fromblast/Statistics_Overall.csv" lines_diff="2"/> 312 <output name="stat_overall" value="results_fromblast/Statistics_Overall.csv" lines_diff="2"/>
261 <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.csv"/> 313 <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.csv"/>
262 </test> 314 </test>
263 </tests> 315 </tests>
264 <help> 316 <help>
265 ====================== 317 ======================
266 OrthoFinder OnlyGroups 318 OrthoFinder OnlyGroups
267 ====================== 319 ======================
268 320