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comparison logex.xml @ 3:f1f6bc33ad2e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
author iuc
date Sat, 10 May 2025 09:08:37 +0000
parents 52ae020a27eb
children ee15b385e5d2
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2:52ae020a27eb 3:f1f6bc33ad2e
1 <tool id="fastk_logex" name="FastK Logex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2" license="MIT"> 1 <tool id="fastk_logex" name="FastK Logex" version="@TOOL_VERSION@+galaxy3" profile="24.2" license="MIT">
2 <description>Performs binary operations on the generated Ktab files from FASTK suite</description> 2 <description>Performs binary operations on the generated Ktab files from FASTK suite</description>
3 <macros> 3 <macros>
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 mkdir -p logex_ktabs 9 mkdir -p logex_ktabs &&
10 && mkdir -p input_files 10 mkdir -p input_files &&
11 && cp '$input_ktab1' input_files/input1.ktab 11 #if $input_type.input_type_selector != 'collection'
12 && ln -s '$input_ktab1_tar' input1.tar 12 cp '$input_ktab1' input_files/input1.ktab &&
13 && tar -xf input1.tar 13 ln -s '$input_ktab1_tar' input1.tar &&
14 && mv ktabfiles ktabfiles_in1 14 tar -xf input1.tar &&
15 && mv "\$(find ktabfiles_in1 -type f -name '*.ktab.1')" "ktabfiles_in1/.input1.ktab.1" 15 mv ktabfiles ktabfiles_in1 &&
16 && cp '$input_ktab2' input_files/input2.ktab 16 mv "\$(find ktabfiles_in1 -type f -name '*.ktab.1')" "ktabfiles_in1/.input1.ktab.1" &&
17 && ln -s '$input_ktab2_tar' input2.tar 17 cp '$input_ktab2' input_files/input2.ktab &&
18 && tar -xf input2.tar 18 ln -s '$input_ktab2_tar' input2.tar &&
19 && mv ktabfiles ktabfiles_in2 19 tar -xf input2.tar &&
20 && mv "\$(find ktabfiles_in2 -type f -name '*.ktab.1')" "ktabfiles_in2/.input2.ktab.1" 20 mv ktabfiles ktabfiles_in2 &&
21 && mv ktabfiles_in1/.input1.ktab.1 input_files/ 21 mv "\$(find ktabfiles_in2 -type f -name '*.ktab.1')" "ktabfiles_in2/.input2.ktab.1" &&
22 && mv ktabfiles_in2/.input2.ktab.1 input_files/ && 22 mv ktabfiles_in1/.input1.ktab.1 input_files/ &&
23 #if $operation_selector == 'and': 23 mv ktabfiles_in2/.input2.ktab.1 input_files/ &&
24 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&.B' input_files/input1.ktab input_files/input2.ktab 24 #if $input_type.operation_selector == 'and'
25 #elif $operation_selector == 'or': 25 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&.B' input_files/input1.ktab input_files/input2.ktab &&
26 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A|.B' input_files/input1.ktab input_files/input2.ktab 26 #elif $input_type.operation_selector == 'or'
27 #elif $operation_selector == 'minus': 27 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A|.B' input_files/input1.ktab input_files/input2.ktab &&
28 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A-B' input_files/input1.ktab input_files/input2.ktab 28 #elif $input_type.operation_selector == 'minus'
29 #elif $operation_selector == 'xor': 29 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A-B' input_files/input1.ktab input_files/input2.ktab &&
30 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A^B' input_files/input1.ktab input_files/input2.ktab 30 #elif $input_type.operation_selector == 'xor'
31 #elif $operation_selector == 'unionsum': 31 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A^B' input_files/input1.ktab input_files/input2.ktab &&
32 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&+B' input_files/input1.ktab input_files/input2.ktab 32 #elif $input_type.operation_selector == 'unionsum'
33 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&+B' input_files/input1.ktab input_files/input2.ktab &&
34 #end if
35 #else
36 #for $i, $j in enumerate($input_type.input_ktab_collection):
37 cp "$j" input_files/${i+1}.ktab &&
38 #end for
39 #for $p, $q in enumerate($input_type.input_ktab_collection_tar):
40 ln -s "$q" input_files/input_ktab_${p+1}.tar &&
41 tar -tf input_files/input_ktab_${p+1}.tar | grep '/\.[^/]*$' | tar --strip-components=1 -xf input_files/input_ktab_${p+1}.tar -C input_files/ -T - &&
42 rm input_files/input_ktab_${p+1}.tar &&
43 #end for
44 COUNT=\$(ls -1 input_files/*.ktab 2>/dev/null | wc -l) &&
45 if [ "\$COUNT" -ge 2 ]; then
46 #if $input_type.operation_sel.operation_selector_collection == 'unionsum':
47 EXPRESSION="out=\$(seq -s '&+' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&
48 #elif $input_type.operation_sel.operation_selector_collection == 'and':
49 EXPRESSION="out=\$(seq -s '&.' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&
50 #elif $input_type.operation_sel.operation_selector_collection == 'minus':
51 EXPRESSION="out=\$(seq -s '-' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&
52 #elif $input_type.operation_sel.operation_selector_collection == 'or':
53 EXPRESSION="out=\$(seq -s '|.' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&
54 #elif $input_type.operation_sel.operation_selector_collection == 'xor':
55 EXPRESSION="out=\$(seq -s '^' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&
56 #elif $input_type.operation_sel.operation_selector_collection == 'custom':
57 EXPRESSION="out=$input_type.operation_sel.custom_expression" &&
58 #end if
59 Logex -T\${GALAXY_SLOTS:-8} -h "\$EXPRESSION" input_files/*.ktab;
60 else
61 echo "ERROR: Logex needs atleast 2 Ktab files" >&2 && exit 1;
62 fi &&
33 #end if 63 #end if
34 && cp *.ktab logex_ktabs/ 64 cp *.ktab logex_ktabs/ &&
35 && cp .*.ktab* logex_ktabs/ 65 cp .*.ktab* logex_ktabs/ &&
36 && tar -cf logex_ktab.tar input_files/ logex_ktabs/ 66 tar -cf logex_ktab.tar input_files/ logex_ktabs/
37 ]]></command> 67 ]]></command>
38 <inputs> 68 <inputs>
39 <param name="input_ktab1" type="data" format="fastk_ktab" label="Input FastK ktab file (first)"/> 69 <conditional name="input_type">
40 <param name="input_ktab1_tar" type="data" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/> 70 <param name="input_type_selector" type="select" label="Single Ktab file or Ktab Collection">
41 <param name="input_ktab2" type="data" format="fastk_ktab" label="Input FastK ktab file (second)"/> 71 <option value="single">Single Ktab file</option>
42 <param name="input_ktab2_tar" type="data" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/> 72 <option value="collection">Ktab files Collection</option>
43 <param name="operation_selector" type="select" label="Select Operation to Perform" help="Select the operation to be performed on the input ktab files."> 73 </param>
44 <option value="and">AND</option> 74 <when value="single">
45 <option value="or">OR</option> 75 <param name="input_ktab1" type="data" format="fastk_ktab" label="Input FastK ktab file (first)"/>
46 <option value="minus">Minus</option> 76 <param name="input_ktab1_tar" type="data" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
47 <option value="unionsum">Unionsum</option> 77 <param name="input_ktab2" type="data" format="fastk_ktab" label="Input FastK ktab file (second)"/>
48 <option value="xor">XOR</option> 78 <param name="input_ktab2_tar" type="data" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
49 </param> 79 <param name="operation_selector" type="select" label="Select Operation to Perform" help="Select the operation to be performed on the input ktab files.">
80 <option value="and">AND</option>
81 <option value="or">OR</option>
82 <option value="minus">Minus</option>
83 <option value="unionsum">Unionsum</option>
84 <option value="xor">XOR</option>
85 </param>
86 </when>
87 <when value="collection">
88 <param name="input_ktab_collection" type="data_collection" collection_type="list" format="fastk_ktab" label="Input FastK ktab Collection"/>
89 <param name="input_ktab_collection_tar" type="data_collection" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
90 <conditional name="operation_sel">
91 <param name="operation_selector_collection" type="select" label="Select Operation to Perform" help="Select the operation to be performed on the input ktab files.">
92 <option value="and">AND</option>
93 <option value="or">OR</option>
94 <option value="minus">Minus</option>
95 <option value="unionsum">Unionsum</option>
96 <option value="xor">XOR</option>
97 <option value="custom">Custom Logical Expression</option>
98 </param>
99 <when value="and"/>
100 <when value="or"/>
101 <when value="minus"/>
102 <when value="unionsum"/>
103 <when value="xor"/>
104 <when value="custom">
105 <param name="custom_expression" type="text" label="Custom Logical Expression" value="out=" help="Enter a custom logical expression based on number of your input ktab files. For Eg: For 3 Ktab files the expression can be out=(A^B)-C">
106 <sanitizer invalid_char="">
107 <valid>
108 <add value="+"/>
109 <add value="-"/>
110 <add value="|"/>
111 <add value="."/>
112 <add value="^"/>
113 <add value="="/>
114 <add value="&amp;"/>
115 </valid>
116 </sanitizer>
117 </param>
118 </when>
119 </conditional>
120 </when>
121 </conditional>
50 </inputs> 122 </inputs>
51 <outputs> 123 <outputs>
52 <data name="fastk_hist_out" format="fastk_hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Logex .hist file"/> 124 <data name="fastk_hist_out" format="fastk_hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Logex .hist file"/>
53 <data name="fastk_ktab_out" format="fastk_ktab" from_work_dir="out.ktab" label="${tool.name} on ${on_string}: Logex .ktab file"/> 125 <data name="fastk_ktab_out" format="fastk_ktab" from_work_dir="out.ktab" label="${tool.name} on ${on_string}: Logex .ktab file"/>
54 <data name="fastk_ktab_files" format="fastk_ktab_tar" from_work_dir="logex_ktab.tar" label="${tool.name} on ${on_string}: FastK Logex ktab files"/> 126 <data name="fastk_ktab_files" format="fastk_ktab_tar" from_work_dir="logex_ktab.tar" label="${tool.name} on ${on_string}: FastK Logex ktab files"/>
55 </outputs> 127 </outputs>
56 <tests> 128 <tests>
57 <test expect_num_outputs="3"> 129 <test expect_num_outputs="3">
58 <param name="input_ktab1" value="fastq1.ktab"/> 130 <conditional name="input_type">
59 <param name="input_ktab1_tar" value="fastk_in1.tar"/> 131 <param name="input_type_selector" value="single"/>
60 <param name="input_ktab2" value="fastq2.ktab"/> 132 <param name="input_ktab1" value="fastq1.ktab"/>
61 <param name="input_ktab2_tar" value="fastk_in2.tar"/> 133 <param name="input_ktab1_tar" value="fastk_in1.tar"/>
62 <param name="operation_selector" value="AND"/> 134 <param name="input_ktab2" value="fastq2.ktab"/>
135 <param name="input_ktab2_tar" value="fastk_in2.tar"/>
136 <param name="operation_selector" value="and"/>
137 </conditional>
63 <output name="fastk_hist_out" ftype="fastk_hist"> 138 <output name="fastk_hist_out" ftype="fastk_hist">
64 <assert_contents> 139 <assert_contents>
65 <has_size value="262164"/> 140 <has_size value="262164"/>
66 </assert_contents> 141 </assert_contents>
67 </output> 142 </output>
76 <has_archive_member path="logex_ktabs/.out.ktab.1"/> 151 <has_archive_member path="logex_ktabs/.out.ktab.1"/>
77 <has_archive_member path="input_files/input1.ktab"/> 152 <has_archive_member path="input_files/input1.ktab"/>
78 <has_archive_member path="input_files/.input1.ktab.1"/> 153 <has_archive_member path="input_files/.input1.ktab.1"/>
79 <has_archive_member path="input_files/input2.ktab"/> 154 <has_archive_member path="input_files/input2.ktab"/>
80 <has_archive_member path="input_files/.input2.ktab.1"/> 155 <has_archive_member path="input_files/.input2.ktab.1"/>
156 </assert_contents>
157 </output>
158 </test>
159 <test expect_num_outputs="3">
160 <conditional name="input_type">
161 <param name="input_type_selector" value="collection"/>
162 <param name="input_ktab_collection">
163 <collection type="list">
164 <element name="input1" value="fastq1.ktab"/>
165 <element name="input2" value="fastq2.ktab"/>
166 </collection>
167 </param>
168 <param name="input_ktab_collection_tar">
169 <collection type="list">
170 <element name="input1" value="fastk_in1.tar"/>
171 <element name="input2" value="fastk_in2.tar"/>
172 </collection>
173 </param>
174 <conditional name="operation_sel">
175 <param name="operation_selector_collection" value="and"/>
176 </conditional>
177 </conditional>
178 <output name="fastk_hist_out" ftype="fastk_hist">
179 <assert_contents>
180 <has_size value="262164"/>
181 </assert_contents>
182 </output>
183 <output name="fastk_ktab_out" ftype="fastk_ktab">
184 <assert_contents>
185 <has_size value="2064"/>
186 </assert_contents>
187 </output>
188 <output name="fastk_ktab_files" ftype="fastk_ktab_tar">
189 <assert_contents>
190 <has_archive_member path="logex_ktabs/out.ktab"/>
191 <has_archive_member path="logex_ktabs/.out.ktab.1"/>
192 <has_archive_member path="input_files/1.ktab"/>
193 <has_archive_member path="input_files/.1.ktab.1"/>
194 <has_archive_member path="input_files/2.ktab"/>
195 <has_archive_member path="input_files/.2.ktab.1"/>
196 </assert_contents>
197 </output>
198 </test>
199 <test expect_num_outputs="3">
200 <conditional name="input_type">
201 <param name="input_type_selector" value="collection"/>
202 <param name="input_ktab_collection">
203 <collection type="list">
204 <element name="input1" value="fastq1.ktab"/>
205 <element name="input2" value="fastq2.ktab"/>
206 </collection>
207 </param>
208 <param name="input_ktab_collection_tar">
209 <collection type="list">
210 <element name="input1" value="fastk_in1.tar"/>
211 <element name="input2" value="fastk_in2.tar"/>
212 </collection>
213 </param>
214 <conditional name="operation_sel">
215 <param name="operation_selector_collection" value="unionsum"/>
216 </conditional>
217 </conditional>
218 <output name="fastk_hist_out" ftype="fastk_hist">
219 <assert_contents>
220 <has_size value="262164"/>
221 </assert_contents>
222 </output>
223 <output name="fastk_ktab_out" ftype="fastk_ktab">
224 <assert_contents>
225 <has_size value="2064"/>
226 </assert_contents>
227 </output>
228 <output name="fastk_ktab_files" ftype="fastk_ktab_tar">
229 <assert_contents>
230 <has_archive_member path="logex_ktabs/out.ktab"/>
231 <has_archive_member path="logex_ktabs/.out.ktab.1"/>
232 <has_archive_member path="input_files/1.ktab"/>
233 <has_archive_member path="input_files/.1.ktab.1"/>
234 <has_archive_member path="input_files/2.ktab"/>
235 <has_archive_member path="input_files/.2.ktab.1"/>
236 </assert_contents>
237 </output>
238 </test>
239 <test expect_num_outputs="3">
240 <conditional name="input_type">
241 <param name="input_type_selector" value="collection"/>
242 <param name="input_ktab_collection">
243 <collection type="list">
244 <element name="input1" value="fastq1.ktab"/>
245 <element name="input2" value="fastq2.ktab"/>
246 </collection>
247 </param>
248 <param name="input_ktab_collection_tar">
249 <collection type="list">
250 <element name="input1" value="fastk_in1.tar"/>
251 <element name="input2" value="fastk_in2.tar"/>
252 </collection>
253 </param>
254 <conditional name="operation_sel">
255 <param name="operation_selector_collection" value="custom"/>
256 <param name="custom_expression" value="A&amp;.B"/>
257 </conditional>
258 </conditional>
259 <output name="fastk_hist_out" ftype="fastk_hist">
260 <assert_contents>
261 <has_size value="262164"/>
262 </assert_contents>
263 </output>
264 <output name="fastk_ktab_out" ftype="fastk_ktab">
265 <assert_contents>
266 <has_size value="2064"/>
267 </assert_contents>
268 </output>
269 <output name="fastk_ktab_files" ftype="fastk_ktab_tar">
270 <assert_contents>
271 <has_archive_member path="logex_ktabs/out.ktab"/>
272 <has_archive_member path="logex_ktabs/.out.ktab.1"/>
273 <has_archive_member path="input_files/1.ktab"/>
274 <has_archive_member path="input_files/.1.ktab.1"/>
275 <has_archive_member path="input_files/2.ktab"/>
276 <has_archive_member path="input_files/.2.ktab.1"/>
81 </assert_contents> 277 </assert_contents>
82 </output> 278 </output>
83 </test> 279 </test>
84 </tests> 280 </tests>
85 <help><![CDATA[ 281 <help><![CDATA[
86 282
87 Logex tool can perform operations such as AND, OR, XOR, Minus and Unionsum on the input given input Ktab files. 283 Logex tool can perform operations such as AND, OR, XOR, Minus and Unionsum on the input given input Ktab files.
88 284
89 The tool requires two input Ktab files and their associated files (Generated in the tarball of FASTK tool with .1 extension) as inputs to perform various binary operations. 285 The tool requires two input Ktab files and their associated files (Generated in the tarball of FASTK tool with .1 extension) as inputs to perform various binary operations.
286
287 The tool also supports Ktab file collections as input. The user can select the operation to be performed on the input Ktab files.
90 288
91 ]]></help> 289 ]]></help>
92 <expand macro="citations"/> 290 <expand macro="citations"/>
93 </tool> 291 </tool>