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comparison cutadapt.xml @ 40:aa784cb3810d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 8bdd212b8708a9d080e87303dd543fb93bc05c2f
author iuc
date Mon, 08 Jul 2024 16:21:21 +0000
parents fe74900d6dc7
children
comparison
equal deleted inserted replaced
39:fe74900d6dc7 40:aa784cb3810d
151 #if str($other_trimming_options.shorten_options.shorten_values) == 'True': 151 #if str($other_trimming_options.shorten_options.shorten_values) == 'True':
152 #if str($other_trimming_options.shorten_options.shorten_end) == '3prime' 152 #if str($other_trimming_options.shorten_options.shorten_end) == '3prime'
153 --length=$other_trimming_options.shorten_options.length 153 --length=$other_trimming_options.shorten_options.length
154 #else 154 #else
155 --length=-$other_trimming_options.shorten_options.length 155 --length=-$other_trimming_options.shorten_options.length
156 #end if
157 #end if
158 #if $paired and str($other_trimming_options.shorten_options_r2.shorten_values_r2) == 'True':
159 #if str($other_trimming_options.shorten_options_r2.shorten_end_r2) == '3prime'
160 -L $other_trimming_options.shorten_options_r2.length2
161 #else
162 -L -$other_trimming_options.shorten_options_r2.length2
156 #end if 163 #end if
157 #end if 164 #end if
158 165
159 $filter_options.discard_trimmed 166 $filter_options.discard_trimmed
160 $filter_options.discard_untrimmed 167 $filter_options.discard_untrimmed
276 <param name="action" type="select" label="What to do if a match is found"> 283 <param name="action" type="select" label="What to do if a match is found">
277 <option value="trim" selected="true">Trim: trim adapter and upstream or downstream sequence</option> 284 <option value="trim" selected="true">Trim: trim adapter and upstream or downstream sequence</option>
278 <option value="retain">Retain: the read is trimmed, but the adapter sequence is not removed</option> 285 <option value="retain">Retain: the read is trimmed, but the adapter sequence is not removed</option>
279 <option value="mask">Mask: mask adapters with 'N' characters instead of trimming them</option> 286 <option value="mask">Mask: mask adapters with 'N' characters instead of trimming them</option>
280 <option value="lowercase">Lowercase: convert to lowercase</option> 287 <option value="lowercase">Lowercase: convert to lowercase</option>
288 <option value="crop">Crop: trim upstream and downstream sequences, i.e. retain adapter sequences only</option>
281 <option value="none">None: leave unchanged</option> 289 <option value="none">None: leave unchanged</option>
282 </param> 290 </param>
283 <param argument="--error-rate" type="float" min="0" max="1" value="0.1" label="Maximum error rate" help="Maximum allowed error rate (no. of errors divided by the length of the matching region)." /> 291 <param argument="--error-rate" type="float" min="0" max="1" value="0.1" label="Maximum error rate" help="Maximum allowed error rate (no. of errors divided by the length of the matching region)." />
284 <param argument="--no-indels" type="boolean" checked="false" truevalue="--no-indels" falsevalue="" label="Do not allow indels (Use ONLY with anchored 5' (front) adapters)." help="Do not allow indels in the alignments. That is, allow only mismatches. This option is currently only supported for anchored 5' adapters ('^ADAPTER') (default: both mismatches and indels are allowed)." /> 292 <param argument="--no-indels" type="boolean" checked="false" truevalue="--no-indels" falsevalue="" label="Do not allow indels (Use ONLY with anchored 5' (front) adapters)." help="Do not allow indels in the alignments. That is, allow only mismatches. This option is currently only supported for anchored 5' adapters ('^ADAPTER') (default: both mismatches and indels are allowed)." />
285 <param argument="--times" type="integer" min="1" value="1" label="Match times" help="Try to remove adapters at most COUNT times. Useful when an adapter gets appended multiple times." /> 293 <param argument="--times" type="integer" min="1" value="1" label="Match times" help="Try to remove adapters at most COUNT times. Useful when an adapter gets appended multiple times." />
312 <option value="False" selected="true">Disabled</option> 320 <option value="False" selected="true">Disabled</option>
313 </param> 321 </param>
314 <when value="True"> 322 <when value="True">
315 <param argument="--length" type="integer" value="0" label="Length" help="Shorten reads to this length. This modification is applied after adapter trimming." /> 323 <param argument="--length" type="integer" value="0" label="Length" help="Shorten reads to this length. This modification is applied after adapter trimming." />
316 <param name="shorten_end" type="select" label="End at which to apply the slice"> 324 <param name="shorten_end" type="select" label="End at which to apply the slice">
325 <option value="3prime">3' ends</option>
326 <option value="5prime">5' ends</option>
327 </param>
328 </when>
329 <when value="False">
330 </when>
331 </conditional>
332 <conditional name="shorten_options_r2">
333 <param name="shorten_values_r2" type="select" label="Separate shortening of R2 reads to a fixed length?" help="For paired-end data, shortening of R2 reads can be handled separately. Ignored for single-end data.">
334 <option value="True">Separate shortening of R2 reads</option>
335 <option value="False" selected="true">Treat R2 reads the same as R1 reads</option>
336 </param>
337 <when value="True">
338 <param argument="-L" name="length2" type="integer" value="0" label="Length" help="Shorten R2 reads to this length. This modification is applied after adapter trimming." />
339 <param name="shorten_end_r2" type="select" label="End at which to apply the slice">
317 <option value="3prime">3' ends</option> 340 <option value="3prime">3' ends</option>
318 <option value="5prime">5' ends</option> 341 <option value="5prime">5' ends</option>
319 </param> 342 </param>
320 </when> 343 </when>
321 <when value="False"> 344 <when value="False">
884 <param name="adapter" value="CGTCCGAANTAG"/> 907 <param name="adapter" value="CGTCCGAANTAG"/>
885 </conditional> 908 </conditional>
886 </repeat> 909 </repeat>
887 </section> 910 </section>
888 <section name="adapter_options"> 911 <section name="adapter_options">
912 <param name="action" value="crop"/>
913 </section>
914 <output name="out1" file="cutadapt_action_crop.out" ftype="fastq"/>
915 </test>
916 <test expect_num_outputs="1">
917 <param name="type" value="single" />
918 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
919 <section name="r1">
920 <repeat name="adapters">
921 <conditional name="adapter_source">
922 <param name="adapter_source_list" value="user"/>
923 <param name="adapter" value="CGTCCGAANTAG"/>
924 </conditional>
925 </repeat>
926 </section>
927 <section name="adapter_options">
889 <param name="action" value="none"/> 928 <param name="action" value="none"/>
890 </section> 929 </section>
891 <output name="out1" file="cutadapt_action_none.out" ftype="fastq"/> 930 <output name="out1" file="cutadapt_action_none.out" ftype="fastq"/>
892 </test> 931 </test>
893 <!-- Test revcomp options --> 932 <!-- Test revcomp options -->
905 <section name="adapter_options"> 944 <section name="adapter_options">
906 <param name="revcomp" value="true"/> 945 <param name="revcomp" value="true"/>
907 </section> 946 </section>
908 <output name="out1" file="cutadapt_revcomp.out" ftype="fastq"/> 947 <output name="out1" file="cutadapt_revcomp.out" ftype="fastq"/>
909 </test> 948 </test>
910 <!-- Test minimum lenghth paired-reads --> 949 <!-- Test minimum length paired-reads -->
911 <test expect_num_outputs="2"> 950 <test expect_num_outputs="2">
912 <param name="type" value="paired" /> 951 <param name="type" value="paired" />
913 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" /> 952 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
914 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" /> 953 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
915 <section name="r1"> 954 <section name="r1">
984 <param name="adapter_source_list" value="user"/> 1023 <param name="adapter_source_list" value="user"/>
985 <param name="adapter" value="AGATCGGAAGAGC"/> 1024 <param name="adapter" value="AGATCGGAAGAGC"/>
986 </conditional> 1025 </conditional>
987 </repeat> 1026 </repeat>
988 </section> 1027 </section>
989 <section name="r2">
990 <repeat name="adapters2">
991 <conditional name="adapter_source2">
992 <param name="adapter_source_list2" value="user"/>
993 <param name="adapter2" value="AGATCGGAAGAGC"/>
994 </conditional>
995 </repeat>
996 </section>
997 <section name="filter_options"> 1028 <section name="filter_options">
998 <param name="pair_filter" value="both"/> 1029 <param name="pair_filter" value="both"/>
999 <param name="minimum_length" value="10"/> 1030 <param name="minimum_length" value="10"/>
1000 <param name="maximum_length" value="50"/> 1031 <param name="maximum_length" value="50"/>
1001 <param name="maximum_length2" value="30"/> 1032 <param name="maximum_length2" value="30"/>
1015 <section name="r1"> 1046 <section name="r1">
1016 <repeat name="adapters"> 1047 <repeat name="adapters">
1017 <conditional name="adapter_source"> 1048 <conditional name="adapter_source">
1018 <param name="adapter_source_list" value="user"/> 1049 <param name="adapter_source_list" value="user"/>
1019 <param name="adapter" value="AGATCGGAAGAGC"/> 1050 <param name="adapter" value="AGATCGGAAGAGC"/>
1020 </conditional>
1021 </repeat>
1022 </section>
1023 <section name="r2">
1024 <repeat name="adapters2">
1025 <conditional name="adapter_source2">
1026 <param name="adapter_source_list2" value="user"/>
1027 <param name="adapter2" value="AGATCGGAAGAGC"/>
1028 </conditional> 1051 </conditional>
1029 </repeat> 1052 </repeat>
1030 </section> 1053 </section>
1031 <section name="filter_options"> 1054 <section name="filter_options">
1032 <param name="pair_filter" value="both"/> 1055 <param name="pair_filter" value="both"/>
1086 </section> 1109 </section>
1087 <section name="filter_options"> 1110 <section name="filter_options">
1088 <param name="minimum_length" value="0"/> 1111 <param name="minimum_length" value="0"/>
1089 </section> 1112 </section>
1090 <output name="out1" file="cutadapt_shorten_5prime.out" ftype="fastq"/> 1113 <output name="out1" file="cutadapt_shorten_5prime.out" ftype="fastq"/>
1114 </test>
1115 <test expect_num_outputs="2">
1116 <param name="type" value="paired" />
1117 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
1118 <section name="r1">
1119 <repeat name="adapters">
1120 <conditional name="adapter_source">
1121 <param name="adapter_source_list" value="user"/>
1122 <param name="adapter" value="AGCCGCTANGACG"/>
1123 </conditional>
1124 </repeat>
1125 </section>
1126 <section name="r2">
1127 <repeat name="adapters2">
1128 <conditional name="adapter_source">
1129 <param name="adapter_source_list" value="user"/>
1130 <param name="adapter" value="AGCCGCTANGACG"/>
1131 </conditional>
1132 </repeat>
1133 </section>
1134 <section name="other_trimming_options">
1135 <conditional name="shorten_options">
1136 <param name="shorten_values" value="True"/>
1137 <param name="shorten_end" value="3prime"/>
1138 <param name="length" value="10"/>
1139 </conditional>
1140 <conditional name="shorten_options_r2">
1141 <param name="shorten_values_r2" value="True"/>
1142 <param name="shorten_end_r2" value="5prime"/>
1143 <param name="length2" value="10"/>
1144 </conditional>
1145 </section>
1146 <section name="filter_options">
1147 <param name="minimum_length" value="0"/>
1148 </section>
1149 <output name="out1" file="cutadapt_shorten_3prime.out" ftype="fastq"/>
1150 <output name="out2" file="cutadapt_shorten_5prime.out" ftype="fastq"/>
1151 </test>
1152 <test expect_num_outputs="2">
1153 <param name="type" value="paired" />
1154 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
1155 <section name="r2">
1156 <repeat name="adapters2">
1157 <conditional name="adapter_source">
1158 <param name="adapter_source_list" value="user"/>
1159 <param name="adapter" value="AGCCGCTANGACG"/>
1160 </conditional>
1161 </repeat>
1162 </section>
1163 <section name="other_trimming_options">
1164 <conditional name="shorten_options_r2">
1165 <param name="shorten_values_r2" value="True"/>
1166 <param name="shorten_end_r2" value="3prime"/>
1167 <param name="length2" value="10"/>
1168 </conditional>
1169 </section>
1170 <section name="filter_options">
1171 <param name="minimum_length" value="0"/>
1172 </section>
1173 <output name="out1" file="cutadapt_small.fastq" ftype="fastq"/>
1174 <output name="out2" file="cutadapt_shorten_3prime.out" ftype="fastq"/>
1091 </test> 1175 </test>
1092 <!-- Test max expected errors options --> 1176 <!-- Test max expected errors options -->
1093 <test expect_num_outputs="1"> 1177 <test expect_num_outputs="1">
1094 <param name="type" value="single" /> 1178 <param name="type" value="single" />
1095 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" /> 1179 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />