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comparison yahs.xml @ 3:39495e107274 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 968382ccb84765d3e8a6e67c43f095a8cc5ab8f5
author iuc
date Wed, 28 Sep 2022 09:41:02 +0000
parents fc925f53cae7
children 425e63adcc5d
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2:fc925f53cae7 3:39495e107274
1 <tool id="yahs" name="YAHS" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> 1 <tool id="yahs" name="YAHS" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>yet another HI-C scaffolding tool</description> 2 <description>yet another HI-C scaffolding tool</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">1.2a</token> 4 <token name="@VERSION@">1.2a.2</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@VERSION@">yahs</requirement> 8 <requirement type="package" version="@VERSION@">yahs</requirement>
9 <requirement type="package" version="1.11">samtools</requirement> 9 <requirement type="package" version="1.11">samtools</requirement>
10 <requirement type="package" version="3.9">python</requirement> 10 <requirement type="package" version="3.9">python</requirement>
20 #if $function.agp: 20 #if $function.agp:
21 ln -s '$function.agp' input.agp && 21 ln -s '$function.agp' input.agp &&
22 #end if 22 #end if
23 samtools faidx input.fasta && 23 samtools faidx input.fasta &&
24 mkdir initial_break agp_out agp_break final_outs && 24 mkdir initial_break agp_out agp_break final_outs &&
25 yahs input.fasta 25 yahs --no-mem-check input.fasta
26 #if $function.bfile.ext == "bam": 26 #if $function.bfile.ext == "bam":
27 input.bam 27 input.bam
28 #else if $function.bfile.ext == "bed": 28 #else if $function.bfile.ext == "bed":
29 input.bed 29 input.bed
30 #end if 30 #end if
150 <data format="txt" name="log_file" from_work_dir="output.log" label="${tool.name} ${on_string}, log file"> 150 <data format="txt" name="log_file" from_work_dir="output.log" label="${tool.name} ${on_string}, log file">
151 <filter>log_out</filter> 151 <filter>log_out</filter>
152 </data> 152 </data>
153 </outputs> 153 </outputs>
154 <tests> 154 <tests>
155 <!-- TEST 1 -->
155 <test expect_num_outputs="5"> 156 <test expect_num_outputs="5">
156 <conditional name="function"> 157 <conditional name="function">
157 <param name="function_select" value="yahs"/> 158 <param name="function_select" value="yahs"/>
158 <param name="fasta" value="test.fasta"/> 159 <param name="fasta" value="test.fasta"/>
159 <param name="bfile" value="test.bed"/> 160 <param name="bfile" value="test.bed"/>
162 </conditional> 163 </conditional>
163 <output name="final_agp_out" file="test_01_scaffolds_final.agp" ftype="agp"/> 164 <output name="final_agp_out" file="test_01_scaffolds_final.agp" ftype="agp"/>
164 <output name="final_fasta_out" file="test_01_scaffolds_final.fa" ftype="fasta"/> 165 <output name="final_fasta_out" file="test_01_scaffolds_final.fa" ftype="fasta"/>
165 <!-- COMMAND: yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 --> 166 <!-- COMMAND: yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 -->
166 </test> 167 </test>
168 <!-- TEST 2 -->
167 <test expect_num_outputs="5"> 169 <test expect_num_outputs="5">
168 <conditional name="function"> 170 <conditional name="function">
169 <param name="function_select" value="yahs"/> 171 <param name="function_select" value="yahs"/>
170 <param name="fasta" value="test.fasta"/> 172 <param name="fasta" value="test.fasta"/>
171 <param name="bfile" value="test.bed"/> 173 <param name="bfile" value="test.bed"/>
177 <output_collection name="agp_break"> 179 <output_collection name="agp_break">
178 <element name="yahs_out_no_break" file="test_02_no_break.agp" ftype="agp"/> 180 <element name="yahs_out_no_break" file="test_02_no_break.agp" ftype="agp"/>
179 </output_collection> 181 </output_collection>
180 <!-- COMMAND: yahs test.fasta test.bed -\-no-contig-ec -\-no-scaffold-ec -o test_2 --> 182 <!-- COMMAND: yahs test.fasta test.bed -\-no-contig-ec -\-no-scaffold-ec -o test_2 -->
181 </test> 183 </test>
184 <!-- TEST 3 -->
185 <test expect_num_outputs="6">
186 <conditional name="function">
187 <param name="function_select" value="yahs"/>
188 <param name="fasta" value="test2.fasta"/>
189 <param name="bfile" value="test2.bam"/>
190 <param name="res" value="1000,2000,5000,10000,20000,50000,100000,200000,500000"/>
191 <conditional name="enzyme_conditional">
192 <param name="enzyme_options" value="not_specified"/>
193 </conditional>
194 </conditional>
195 <param name="log_out" value="yes"/>
196 <output name="log_file" ftype="txt">
197 <assert_contents>
198 <has_text text="[I::dump_links_from_bam_file] dumped 6399 read pairs from 17675 records: 6297 intra links + 102 inter links" />
199 </assert_contents>
200 </output>
201 <!-- COMMAND: yahs test.fasta test.bam -r 1000,2000,5000,10000,20000,50000,100000,200000,500000 -o test_3 -->
202 </test>
203 <!-- TEST 4 -->
182 <test expect_num_outputs="5"> 204 <test expect_num_outputs="5">
183 <conditional name="function"> 205 <conditional name="function">
184 <param name="function_select" value="yahs"/> 206 <param name="function_select" value="yahs"/>
185 <param name="fasta" value="test.fasta"/> 207 <param name="fasta" value="test2.fasta"/>
186 <param name="bfile" value="test.bam"/> 208 <param name="bfile" value="test2.bed"/>
187 <param name="qual" value="10"/> 209 <param name="qual" value="10"/>
188 <param name="length" value="20"/> 210 <param name="length" value="20"/>
189 <conditional name="enzyme_conditional"> 211 <conditional name="enzyme_conditional">
190 <param name="enzyme_options" value="specific"/> 212 <param name="enzyme_options" value="not_specified"/>
191 <param name="manual_enzyme" value="GATC,GANT"/>
192 </conditional> 213 </conditional>
193 </conditional> 214 </conditional>
194 <output name="final_agp_out" file="test_03_scaffolds_final.agp" ftype="agp"/> 215 <output name="final_agp_out" file="test_04_scaffolds_final.agp" ftype="agp"/>
195 <output name="final_fasta_out" file="test_03_scaffolds_final.fa" ftype="fasta"/> 216 <output name="final_fasta_out" file="test_04_scaffolds_final.fa" ftype="fasta"/>
196 <output_collection name="initial_agp_break">
197 <element name="yahs_out_inital_break_01" file="test_03_initial_break.agp" ftype="agp"/>
198 </output_collection>
199 <!-- COMMAND: yahs test.fasta test.bed -q 10 -l 20 -e 'GATC,GANT' -o test_3 -->
200 </test>
201 <test expect_num_outputs="5">
202 <conditional name="function">
203 <param name="function_select" value="yahs"/>
204 <param name="fasta" value="test.fasta"/>
205 <param name="bfile" value="test.bam"/>
206 <param name="qual" value="10"/>
207 <param name="length" value="20"/>
208 <conditional name="enzyme_conditional">
209 <param name="enzyme_options" value="preconfigured"/>
210 <param name="preconfigured_enzymes" value="arima1"/>
211 </conditional>
212 </conditional>
213 <output name="final_agp_out" file="test_03_scaffolds_final.agp" ftype="agp"/>
214 <output name="final_fasta_out" file="test_03_scaffolds_final.fa" ftype="fasta"/>
215 <output_collection name="initial_agp_break"> 217 <output_collection name="initial_agp_break">
216 <element name="yahs_out_inital_break_01" file="test_04_initial_break.agp" ftype="agp"/> 218 <element name="yahs_out_inital_break_01" file="test_04_initial_break.agp" ftype="agp"/>
217 </output_collection> 219 </output_collection>
218 <!-- COMMAND: yahs test.fasta test.bed -q 10 -l 20 -e 'GATC,GANT' -o test_3 --> 220 </test>
219 </test> 221 <!-- TEST 5 -->
220 <test expect_num_outputs="1"> 222 <test expect_num_outputs="1">
221 <conditional name="function"> 223 <conditional name="function">
222 <param name="function_select" value="agp_to_fasta"/> 224 <param name="function_select" value="agp_to_fasta"/>
223 <param name="fasta" value="test.fasta"/> 225 <param name="fasta" value="test.fasta"/>
224 <param name="agp" value="test.agp"/> 226 <param name="agp" value="test.agp"/>
225 <param name="length" value="20"/> 227 <param name="length" value="20"/>
226 </conditional> 228 </conditional>
227 <output name="fasta_from_agp" file="test_05.fasta" ftype="fasta"/> 229 <output name="fasta_from_agp" file="test_05.fasta" ftype="fasta"/>
228 <!-- COMMAND: agp_to_fasta test.fasta test.agp -l 20 -o test_4 --> 230 <!-- COMMAND: agp_to_fasta test.fasta test.agp -l 20 -o test_4 -->
229 </test> 231 </test>
232 <!-- TEST 6 -->
230 <test expect_num_outputs="6"> 233 <test expect_num_outputs="6">
231 <conditional name="function"> 234 <conditional name="function">
232 <param name="function_select" value="yahs"/> 235 <param name="function_select" value="yahs"/>
233 <param name="fasta" value="test.fasta"/> 236 <param name="fasta" value="test.fasta"/>
234 <param name="bfile" value="test.bed"/> 237 <param name="bfile" value="test.bed"/>