Mercurial > repos > galaxy-australia > cactus_cactus

comparison cactus_cactus.xml @ 15:098506c54016 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus commit 8fc43fe1e8c12438a14dbd174a8af3e7cb8b55dc
author iuc
date Thu, 08 Feb 2024 08:52:28 +0000
parents 9eeb13a92d79
children
comparison
equal deleted inserted replaced
14:94b8c6013083 15:098506c54016
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/> 6 <expand macro="xrefs"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 export TMPDIR=\${_GALAXY_JOB_TMP_DIR} &&
10 9
11 ## Set up seqfile 10 ## Set up seqfile
12 11
13 #if $aln_mode.aln_mode_select == 'interspecies': 12 #if $aln_mode.aln_mode_select == 'interspecies':
14 cat $aln_mode.in_tree >> seqfile.txt && 13 cat $aln_mode.in_tree >> seqfile.txt &&
28 ## https://github.com/ComparativeGenomicsToolkit/cactus/issues/1093#issuecomment-1620088688 27 ## https://github.com/ComparativeGenomicsToolkit/cactus/issues/1093#issuecomment-1620088688
29 cactus-pangenome 28 cactus-pangenome
30 --reference $aln_mode.ref_level 29 --reference $aln_mode.ref_level
31 --binariesMode local 30 --binariesMode local
32 --maxCores \${GALAXY_SLOTS:-4} 31 --maxCores \${GALAXY_SLOTS:-4}
33 --maxMemory \${GALAXY_MEMORY_MB:-8192}M 32 --maxMemory \${GALAXY_MEMORY_MB:-16384}M
34 --outDir ./ 33 --outDir ./
35 --outName alignment 34 --outName alignment
36 jobStore 35 jobStore
37 seqfile.txt 36 seqfile.txt
38 #else if $aln_mode.aln_mode_select == 'interspecies': 37 #else if $aln_mode.aln_mode_select == 'interspecies':
39 ## Run cactus normally 38 ## Run cactus normally
40 cactus 39 cactus
41 --binariesMode local 40 --binariesMode local
42 --maxCores \${GALAXY_SLOTS:-4} 41 --maxCores \${GALAXY_SLOTS:-4}
43 --maxMemory \${GALAXY_MEMORY_MB:-8192}M 42 --maxMemory \${GALAXY_MEMORY_MB:-16384}M
44 --workDir ./ 43 --workDir ./
45 jobStore 44 jobStore
46 seqfile.txt 45 seqfile.txt
47 alignment.full.hal 46 alignment.full.hal
48 #end if 47 #end if
53 <param name="aln_mode_select" type="select" label="Alignment mode" help="The taxonomic relationship between input genomes. If genomes are from multiple individuals of the same species, select 'Within-species'"> 52 <param name="aln_mode_select" type="select" label="Alignment mode" help="The taxonomic relationship between input genomes. If genomes are from multiple individuals of the same species, select 'Within-species'">
54 <option value="interspecies" selected="true">Between-species</option> 53 <option value="interspecies" selected="true">Between-species</option>
55 <option value="intraspecies">Within-species</option> 54 <option value="intraspecies">Within-species</option>
56 </param> 55 </param>
57 <when value="interspecies"> 56 <when value="interspecies">
58 <param name="in_tree" type="data" format="nhx" label="Guide tree" help="Phylogenetic tree in Newick format. Required by Cactus to achieve linear scaling with number of input genomes" /> 57 <param name="in_tree" type="data" format="nhx" label="Guide tree" help="Phylogenetic tree in Newick format. Required by Cactus to achieve linear scaling with number of input genomes"/>
59 </when> 58 </when>
60 <when value="intraspecies"> 59 <when value="intraspecies">
61 <param name="ref_level" type="text" value="" label="Reference genome" help="Pangenomes from Minigraph-Cactus depend on a predetermined reference genome. Specify one of the Input Genomes as the reference genome. This must match the label used in 'Genome Label'."> 60 <param name="ref_level" type="text" value="" label="Reference genome" help="Pangenomes from Minigraph-Cactus depend on a predetermined reference genome. Specify one of the Input Genomes as the reference genome. This must match the label used in 'Genome Label'.">
62 <sanitizer invalid_char=""> 61 <sanitizer invalid_char="">
63 <valid initial="string.letters,string.digits"> 62 <valid initial="string.letters,string.digits">
64 <add value="_" /> 63 <add value="_"/>
65 </valid> 64 </valid>
66 </sanitizer> 65 </sanitizer>
67 <validator type="regex">[0-9a-zA-Z_]+</validator> 66 <validator type="regex">[0-9a-zA-Z_]+</validator>
68 </param> 67 </param>
69 </when> 68 </when>
70 </conditional> 69 </conditional>
71 <repeat name="in_seqs" title="Input genome"> 70 <repeat name="in_seqs" title="Input genome">
72 <param name="label" type="text" value="" label="Genome label" help="NO SPACES. Must match a label in the guide tree."> 71 <param name="label" type="text" value="" label="Genome label" help="NO SPACES. Must match a label in the guide tree.">
73 <sanitizer invalid_char=""> 72 <sanitizer invalid_char="">
74 <valid initial="string.letters,string.digits"> 73 <valid initial="string.letters,string.digits">
75 <add value="_" /> 74 <add value="_"/>
76 </valid> 75 </valid>
77 </sanitizer> 76 </sanitizer>
78 <validator type="regex">[0-9a-zA-Z_]+</validator> 77 <validator type="regex">[0-9a-zA-Z_]+</validator>
79 </param> 78 </param>
80 <param name="fasta" type="data" format="fasta,fasta.gz" label="Genome Sequence" help="Input genome"/> 79 <param name="fasta" type="data" format="fasta,fasta.gz" label="Genome Sequence" help="Input genome"/>
83 <!-- root mr --> 82 <!-- root mr -->
84 </inputs> 83 </inputs>
85 <outputs> 84 <outputs>
86 <data name="out_hal" format="h5" from_work_dir="alignment.full.hal" label="${tool.name} on ${on_string} (HAL file)"> 85 <data name="out_hal" format="h5" from_work_dir="alignment.full.hal" label="${tool.name} on ${on_string} (HAL file)">
87 </data> 86 </data>
88 <data name="out_gfa" format="gfa2.gz" from_work_dir="alignment.gfa.gz" label="${tool.name} on ${on_string} (GFA file)" > 87 <data name="out_gfa" format="gfa2.gz" from_work_dir="alignment.gfa.gz" label="${tool.name} on ${on_string} (GFA file)">
89 <filter>aln_mode['aln_mode_select'] == 'intraspecies'</filter> 88 <filter>aln_mode['aln_mode_select'] == 'intraspecies'</filter>
90 </data> 89 </data>
91 </outputs> 90 </outputs>
92 <tests> 91 <tests>
93 <!-- test interspecies mode --> 92 <!-- test interspecies mode -->
116 <param name="label" value="simRat_chr6"/> 115 <param name="label" value="simRat_chr6"/>
117 <param name="fasta" value="simRat_chr6.fasta"/> 116 <param name="fasta" value="simRat_chr6.fasta"/>
118 </repeat> 117 </repeat>
119 <output name="out_hal"> 118 <output name="out_hal">
120 <assert_contents> 119 <assert_contents>
121 <has_size value="4472551" delta="200000" /> 120 <has_size value="4472551" delta="200000"/>
122 </assert_contents> 121 </assert_contents>
123 </output> 122 </output>
124 </test> 123 </test>
125 <!-- within-species mode --> 124 <!-- within-species mode -->
126 <test expect_num_outputs="2"> 125 <test expect_num_outputs="2">
148 <param name="label" value="simRat_chr6"/> 147 <param name="label" value="simRat_chr6"/>
149 <param name="fasta" value="simRat_chr6.fasta"/> 148 <param name="fasta" value="simRat_chr6.fasta"/>
150 </repeat> 149 </repeat>
151 <output name="out_hal"> 150 <output name="out_hal">
152 <assert_contents> 151 <assert_contents>
153 <has_size value="565214" delta="65214" /> 152 <has_size value="565214" delta="65214"/>
154 </assert_contents> 153 </assert_contents>
155 </output> 154 </output>
156 <output name="out_gfa"> 155 <output name="out_gfa">
157 <assert_contents> 156 <assert_contents>
158 <has_size value="173000" delta="200000" /> 157 <has_size value="173000" delta="200000"/>
159 </assert_contents>
160 </output>
161 </test>
162 <!-- compressed input -->
163 <test expect_num_outputs="2">
164 <conditional name="aln_mode">
165 <param name="aln_mode_select" value="intraspecies"/>
166 <param name="ref_level" value="germ_25"/>
167 </conditional>
168 <repeat name="in_seqs">
169 <param name="label" value="germ_25"/>
170 <param name="fasta" value="germ_25.fasta.gz"/>
171 </repeat>
172 <repeat name="in_seqs">
173 <param name="label" value="vulg_25"/>
174 <param name="fasta" value="vulg_25.fasta.gz"/>
175 </repeat>
176 <repeat name="in_seqs">
177 <param name="label" value="pens_25"/>
178 <param name="fasta" value="pens_25.fasta.gz"/>
179 </repeat>
180 <output name="out_hal">
181 <assert_contents>
182 <has_size value="6235006" delta="200000" />
183 </assert_contents>
184 </output>
185 <output name="out_gfa">
186 <assert_contents>
187 <has_size value="5771414" delta="200000" />
188 </assert_contents> 158 </assert_contents>
189 </output> 159 </output>
190 </test> 160 </test>
191 <!-- FASTA header with spaces (used to fail) --> 161 <!-- FASTA header with spaces (used to fail) -->
192 <test expect_num_outputs="2"> 162 <test expect_num_outputs="2">
202 <param name="label" value="badheader2"/> 172 <param name="label" value="badheader2"/>
203 <param name="fasta" value="bh2.fasta.gz"/> 173 <param name="fasta" value="bh2.fasta.gz"/>
204 </repeat> 174 </repeat>
205 <output name="out_hal"> 175 <output name="out_hal">
206 <assert_contents> 176 <assert_contents>
207 <has_size value="3382274" delta="200000" /> 177 <has_size value="3382274" delta="200000"/>
208 </assert_contents> 178 </assert_contents>
209 </output> 179 </output>
210 <output name="out_gfa"> 180 <output name="out_gfa">
211 <assert_contents> 181 <assert_contents>
212 <has_size value="764748" delta="200000" /> 182 <has_size value="764748" delta="200000"/>
213 </assert_contents> 183 </assert_contents>
214 </output> 184 </output>
215 </test> 185 </test>
216 </tests> 186 </tests>
217 <help><![CDATA[ 187 <help><![CDATA[
218 188
219 .. class:: infomark 189 .. class:: infomark
220 190
221 **What it does** 191 **What it does**
222 192