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comparison seqkit_split2.xml @ 1:911de3a36b31 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
author iuc
date Wed, 08 Oct 2025 20:26:20 +0000
parents c19015f577a5
children
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0:c19015f577a5 1:911de3a36b31
1 <tool id="seqkit_split2" name="Seqkit Split2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="seqkit_split2" name="Seqkit Split2" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>Split sequences into files by part size, number of parts, or length</description> 2 <description>Split sequences into files by part size, number of parts, or length</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
64 #else: 64 #else:
65 '$read1' 65 '$read1'
66 #end if 66 #end if
67 #if str($split_type.split_selector) == 'by_part': 67 #if str($split_type.split_selector) == 'by_part':
68 -p $split_type.by_part 68 -p $split_type.by_part
69 #if $paired:
70 --by-part-prefix "seqkit_split2_R{read}_"
71 #end if
69 #else if str($split_type.split_selector) == 'by_size': 72 #else if str($split_type.split_selector) == 'by_size':
70 -s $split_type.by_size 73 -s $split_type.by_size
74 #if $paired:
75 --by-size-prefix string "seqkit_split2_R{read}_"
76 #end if
71 #else if str($split_type.split_selector) == 'by_length': 77 #else if str($split_type.split_selector) == 'by_length':
72 -l $split_type.by_length 78 -l $split_type.by_length
73 #end if 79 #end if
74 -o seqkit_split2 80 -o seqkit_split2
75 -O out 81 -O out
76 -j "\${GALAXY_SLOTS:-4}" 82 -j "\${GALAXY_SLOTS:-4}"
83 #if $paired:
84 && (find out/ -type f -name "seqkit_split2_*.*" | while read -r file; do mv "\$file" "\$(echo \$file | sed -E 's/(seqkit_split2)_(R1|R2)_([0-9]+)(\..+)/\1_\3_\2\4/' | sed -E 's/_R1/_forward/; s/_R2/_reverse/')"; done)
85 #end if
77 ]]></command> 86 ]]></command>
78 <inputs> 87 <inputs>
79 <conditional name="input_file_type"> 88 <conditional name="input_file_type">
80 <param name="type" type="select" label="Single-end or Paired-end reads?"> 89 <param name="type" type="select" label="Single-end or Paired-end reads?">
81 <option value="single">Single-end</option> 90 <option value="single">Single-end</option>
108 </conditional> 117 </conditional>
109 </inputs> 118 </inputs>
110 <outputs> 119 <outputs>
111 <collection name="outputs_files" type="list" label="${tool.name} on ${on_string}: Splitted files"> 120 <collection name="outputs_files" type="list" label="${tool.name} on ${on_string}: Splitted files">
112 <discover_datasets pattern="(?P&lt;designation&gt;seqkit_split2\.part_\d+)\.(?P&lt;ext&gt;.+)" directory="out"/> 121 <discover_datasets pattern="(?P&lt;designation&gt;seqkit_split2\.part_\d+)\.(?P&lt;ext&gt;.+)" directory="out"/>
122 <filter>input_file_type['type'] == 'single' </filter>
123 </collection>
124 <collection name="outputs_paired_files" type="list:paired" label="${tool.name} on ${on_string}: Paired-End Splitted files">
125 <filter>input_file_type['type'] == 'paired_collection' </filter>
126 <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)_(?P&lt;identifier_1&gt;forward|reverse)\.(?P&lt;ext&gt;.+)" directory="out"/>
113 </collection> 127 </collection>
114 </outputs> 128 </outputs>
115 <tests> 129 <tests>
116 <!-- Test 01: for Seqkit Split with Single End FASTQ file; splitting by parts --> 130 <!-- Test 01: for Seqkit Split with Single End FASTQ file; splitting by parts -->
117 <test expect_num_outputs="1"> 131 <test expect_num_outputs="1">
150 </conditional> 164 </conditional>
151 <conditional name="split_type"> 165 <conditional name="split_type">
152 <param name="split_selector" value="by_part"/> 166 <param name="split_selector" value="by_part"/>
153 <param name="by_part" value="2"/> 167 <param name="by_part" value="2"/>
154 </conditional> 168 </conditional>
155 <output_collection name="outputs_files" type="list" count="2"> 169 <output_collection name="outputs_paired_files" type="list:paired" count="2">
156 <element name="seqkit_split2.part_001" ftype="fastqsanger.gz"> 170 <element name="seqkit_split2_001">
157 <assert_contents> 171 <element name="forward" ftype="fastqsanger.gz">
158 <has_n_lines n="4958"/> 172 <assert_contents>
159 </assert_contents> 173 <has_n_lines n="4958"/>
160 </element> 174 </assert_contents>
161 <element name="seqkit_split2.part_002" ftype="fastqsanger.gz"> 175 </element>
162 <assert_contents> 176 <element name="reverse" ftype="fastqsanger.gz">
163 <has_n_lines n="4949"/> 177 <assert_contents>
164 </assert_contents> 178 <has_n_lines n="3792"/>
179 </assert_contents>
180 </element>
181 </element>
182 <element name="seqkit_split2_002">
183 <element name="forward" ftype="fastqsanger.gz">
184 <assert_contents>
185 <has_n_lines n="4949"/>
186 </assert_contents>
187 </element>
188 <element name="reverse" ftype="fastqsanger.gz">
189 <assert_contents>
190 <has_n_lines n="3657"/>
191 </assert_contents>
192 </element>
165 </element> 193 </element>
166 </output_collection> 194 </output_collection>
167 </test> 195 </test>
168 196
169 <!-- Test 03: for Seqkit Split with Single End FASTA file; splitting by parts --> 197 <!-- Test 03: for Seqkit Split with Single End FASTA file; splitting by parts -->