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comparison cutadapt.xml @ 27:de6cebe3c043 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
author iuc
date Mon, 01 Nov 2021 12:14:05 +0000
parents 44e2cc14f75b
children c053d4cad713
comparison
equal deleted inserted replaced
26:44e2cc14f75b 27:de6cebe3c043
77 77
78 cutadapt 78 cutadapt
79 79
80 -j=\${GALAXY_SLOTS:-4} 80 -j=\${GALAXY_SLOTS:-4}
81 81
82 #if 'json_stats' in $output_selector:
83 --json stats.json
84 #end if
85
82 #if str( $library.type ) == "single": 86 #if str( $library.type ) == "single":
83 @read1_options@ 87 @read1_options@
84 #if 'multiple_output' in $output_selector: 88 #if 'multiple_output' in $output_selector:
85 --output='split/{name}.${input_1.ext}' 89 --output='split/{name}.${input_1.ext}'
86 #else: 90 #else:
156 160
157 161
158 '${read1}' 162 '${read1}'
159 #if $paired: 163 #if $paired:
160 '${read2}' 164 '${read2}'
165 #if $library.r2.quality_cutoff2:
166 -Q=$library.r2.quality_cutoff2
167 #end if
161 #end if 168 #end if
162 169
163 #if 'report' in $output_selector: 170 #if 'report' in $output_selector:
164 > report.txt 171 > report.txt
165 #end if 172 #end if
246 <param argument="--discard-cassava" type="boolean" truevalue="--discard-cassava" falsevalue="" checked="False" label="Discard CASAVA filtering" help="Discard reads that did not pass CASAVA filtering (header has :Y:)." /> 253 <param argument="--discard-cassava" type="boolean" truevalue="--discard-cassava" falsevalue="" checked="False" label="Discard CASAVA filtering" help="Discard reads that did not pass CASAVA filtering (header has :Y:)." />
247 </section> 254 </section>
248 255
249 <!-- Read Modification Options --> 256 <!-- Read Modification Options -->
250 <section name="read_mod_options" title="Read Modification Options"> 257 <section name="read_mod_options" title="Read Modification Options">
251 <param argument="--quality-cutoff" type="text" value="0" label="Quality cutoff" help=" Trim low-quality bases from 5' and/or 3' ends of each read before adapter removal. Applied to both reads if data is paired. If one value is given, only the 3' end is trimmed. If two comma-separated cutoffs are given, the 5' end is trimmed with the first cutoff, the 3' end with the second."> 258 <param argument="--quality-cutoff" type="text" value="0" label="Quality cutoff" help=" Trim low-quality bases from 5' and/or 3' ends of each read before adapter removal. Applied to both reads for paired-end data, unless a separate value for the second read is specified. If one value is given, only the 3' end is trimmed. If two comma-separated cutoffs are given, the 5' end is trimmed with the first cutoff, the 3' end with the second.">
252 <sanitizer> 259 <sanitizer>
253 <valid initial="string.digits"><add value="," /></valid> 260 <valid initial="string.digits"><add value="," /></valid>
254 </sanitizer> 261 </sanitizer>
255 <validator type="regex">[0-9,]+</validator> 262 <validator type="regex">[0-9,]+</validator>
256 </param> 263 </param>
308 <option value="wildcard_file">Wildcard file: when the adapter has wildcard bases (Ns) write adapter bases matching wildcard positions.</option> 315 <option value="wildcard_file">Wildcard file: when the adapter has wildcard bases (Ns) write adapter bases matching wildcard positions.</option>
309 <option value="too_short_file">Too short reads: write reads that are too short according to minimum length specified (default: discard reads).</option> 316 <option value="too_short_file">Too short reads: write reads that are too short according to minimum length specified (default: discard reads).</option>
310 <option value="too_long_file">Too long reads: write reads that are too long (according to maximum length specified)</option> 317 <option value="too_long_file">Too long reads: write reads that are too long (according to maximum length specified)</option>
311 <option value="untrimmed_file">Untrimmed reads: write reads that do not contain the adapter to a separate file, instead of writing them to the regular output file (default: output to same file as trimmed)</option> 318 <option value="untrimmed_file">Untrimmed reads: write reads that do not contain the adapter to a separate file, instead of writing them to the regular output file (default: output to same file as trimmed)</option>
312 <option value="multiple_output">Multiple output: create a separate file for each adapter trimmed (default: all trimmed reads are in a single file)</option> 319 <option value="multiple_output">Multiple output: create a separate file for each adapter trimmed (default: all trimmed reads are in a single file)</option>
320 <option value="json_stats">Statistics in JSON format</option>
313 </param> 321 </param>
314 </inputs> 322 </inputs>
315 323
316 <outputs> 324 <outputs>
317 <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output"> 325 <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output">
370 <data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_long_paired_output*" label="${tool.name} on ${on_string}: Too Long Read 2" > 378 <data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_long_paired_output*" label="${tool.name} on ${on_string}: Too Long Read 2" >
371 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter> 379 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
372 <filter>output_selector and 'too_long_file' in output_selector</filter> 380 <filter>output_selector and 'too_long_file' in output_selector</filter>
373 <expand macro="inherit_format_2" /> 381 <expand macro="inherit_format_2" />
374 </data> 382 </data>
375 383 <data name="json_stats" format="json" from_work_dir="stats.json" label="${tool.name} on ${on_string}: Statistics (JSON)" >
376 <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Split outputs" > 384 <filter>output_selector and 'json_stats' in output_selector</filter>
385 </data>
386 <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Split outputs" format="fastqsanger" >
377 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fastq.*)" directory="split" /> 387 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fastq.*)" directory="split" />
378 <filter>output_selector and 'multiple_output' in output_selector</filter> 388 <filter>output_selector and 'multiple_output' in output_selector</filter>
379 </collection> 389 </collection>
380 </outputs> 390 </outputs>
381 391
503 <output name="out1" file="cutadapt_discard.out" ftype="fastq"/> 513 <output name="out1" file="cutadapt_discard.out" ftype="fastq"/>
504 <assert_command> 514 <assert_command>
505 <has_text text="--discard-trimmed"/> 515 <has_text text="--discard-trimmed"/>
506 </assert_command> 516 </assert_command>
507 </test> 517 </test>
508 <!-- Ensure rest file output works --> 518 <!-- Ensure rest file output works, test json output -->
509 <test expect_num_outputs="2"> 519 <test expect_num_outputs="3">
510 <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" /> 520 <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" />
511 <section name="r1"> 521 <section name="r1">
512 <repeat name="adapters"> 522 <repeat name="adapters">
513 <conditional name="adapter_source"> 523 <conditional name="adapter_source">
514 <param name="adapter_source_list" value="user"/> 524 <param name="adapter_source_list" value="user"/>
516 </conditional> 526 </conditional>
517 </repeat> 527 </repeat>
518 </section> 528 </section>
519 <param name="output_filtering" value="default"/> 529 <param name="output_filtering" value="default"/>
520 <param name="read_modification" value="none"/> 530 <param name="read_modification" value="none"/>
521 <param name="output_selector" value="rest_file"/> 531 <param name="output_selector" value="rest_file,json_stats"/>
522 <output name="out1" file="cutadapt_rest.out" ftype="fasta"/> 532 <output name="out1" file="cutadapt_rest.out" ftype="fasta"/>
533 <output name="json_stats" file="cutadapt_rest.json" ftype="json"/>
523 <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/> 534 <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>
524 </test> 535 </test>
525 <!-- Ensure nextseq-trim option works --> 536 <!-- Ensure nextseq-trim option works -->
526 <test expect_num_outputs="1"> 537 <test expect_num_outputs="1">
527 <param name="type" value="single" /> 538 <param name="type" value="single" />
1080 <output name="out1" file="cutadapt_builtin_internal_adapter.out" ftype="fastq"/> 1091 <output name="out1" file="cutadapt_builtin_internal_adapter.out" ftype="fastq"/>
1081 <assert_command> 1092 <assert_command>
1082 <has_text text="TGTAGGCCX"/> 1093 <has_text text="TGTAGGCCX"/>
1083 </assert_command> 1094 </assert_command>
1084 </test> 1095 </test>
1096 <!-- Ensure individual per adapter noindels parameter works -->
1097 <test expect_num_outputs="3">
1098 <param name="type" value="paired_collection" />
1099 <param name="input_1">
1100 <collection type="paired">
1101 <element name="forward" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
1102 <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
1103 </collection>
1104 </param>
1105 <section name="r1">
1106 <repeat name="adapters">
1107 <conditional name="adapter_source">
1108 <param name="adapter_source_list" value="user"/>
1109 <param name="adapter" value="AGATCGGAAGAGC"/>
1110 </conditional>
1111 <param name="single_noindels" value=";noindels" />
1112 </repeat>
1113 </section>
1114 <section name="r2">
1115 <repeat name="adapters2">
1116 <conditional name="adapter_source2">
1117 <param name="adapter_source_list2" value="user"/>
1118 <param name="adapter2" value="AGATCGGAAGAGC"/>
1119 </conditional>
1120 <param name="single_noindels" value=";noindels" />
1121 </repeat>
1122 </section>
1123 <output_collection name="out_pairs" type="paired">
1124 <element name="forward" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz" />
1125 <element name="reverse" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz" />
1126 </output_collection>
1127 </test>
1128 <!-- Ensure specifying quality cutoff (for both reads) works -->
1129 <test expect_num_outputs="3">
1130 <param name="type" value="paired_collection" />
1131 <param name="input_1">
1132 <collection type="paired">
1133 <element name="forward" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
1134 <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
1135 </collection>
1136 </param>
1137 <param name="quality_cutoff" value="5" />
1138 <section name="r1">
1139 <repeat name="adapters">
1140 <conditional name="adapter_source">
1141 <param name="adapter_source_list" value="user"/>
1142 <param name="adapter" value="AGATCGGAAGAGC"/>
1143 </conditional>
1144 </repeat>
1145 </section>
1146 <section name="r2">
1147 <repeat name="adapters2">
1148 <conditional name="adapter_source2">
1149 <param name="adapter_source_list2" value="user"/>
1150 <param name="adapter2" value="AGATCGGAAGAGC"/>
1151 </conditional>
1152 </repeat>
1153 <param name="quality_cutoff2" value="15,20"/>
1154 </section>
1155 <output_collection name="out_pairs" type="paired">
1156 <element name="forward" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz" />
1157 <element name="reverse" decompress="True" file="cutadapt_out2_cutoff.fq.gz" ftype="fastq.gz" />
1158 </output_collection>
1159 </test>
1085 </tests> 1160 </tests>
1086 1161
1087 <help><![CDATA[ 1162 <help><![CDATA[
1088 1163
1089 .. class:: infomark 1164 .. class:: infomark