Mercurial > repos > iuc > last
comparison lastdb.xml @ 2:bf30030e5265 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db"
| author | iuc |
|---|---|
| date | Thu, 10 Sep 2020 16:08:15 +0000 |
| parents | 86206f93fb13 |
| children | 8705e0d74a0f |
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| 1:86206f93fb13 | 2:bf30030e5265 |
|---|---|
| 9 <requirements> | 9 <requirements> |
| 10 <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement> | 10 <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement> |
| 11 </requirements> | 11 </requirements> |
| 12 | 12 |
| 13 <command detect_errors="exit_code"><![CDATA[ | 13 <command detect_errors="exit_code"><![CDATA[ |
| 14 lastdb | 14 lastdb |
| 15 -Q $lastdb.Q | 15 |
| 16 #if $input_files.ext == 'fasta' | |
| 17 -Q 0 | |
| 18 #else if $input_files.ext == 'fastqsanger' | |
| 19 -Q 1 | |
| 20 #else if $input_files.ext == 'fastqsolexa' | |
| 21 -Q 2 | |
| 22 #else if $input_files.ext == 'fastqillumina' | |
| 23 -Q 3 | |
| 24 #end if | |
| 16 $lastdb.sequences_type.protein | 25 $lastdb.sequences_type.protein |
| 17 -a $lastdb.sequences_type.a | 26 -a $lastdb.sequences_type.a |
| 18 -R $lastdb.repeats.uppercase$lastdb.repeats.simple_repeat | 27 -R $lastdb.repeats.uppercase$lastdb.repeats.simple_repeat |
| 19 $lastdb.repeats.sm_lower | 28 $lastdb.repeats.sm_lower |
| 20 -S $lastdb.lastdb_advanced.S | 29 -S $lastdb.lastdb_advanced.S |
| 30 '$input_files' | 39 '$input_files' |
| 31 | 40 |
| 32 && | 41 && |
| 33 | 42 |
| 34 mkdir '$outfile.files_path' && | 43 mkdir '$outfile.files_path' && |
| 35 mv lastdb.* '$outfile.files_path' | 44 mv lastdb* '$outfile.files_path' |
| 36 ]]></command> | 45 ]]></command> |
| 37 | 46 |
| 38 <inputs> | 47 <inputs> |
| 39 <param name="input_files" type="data" format="fasta,fastqsanger,fastqsolexa,fastqillumina" label="Reference(s) input files" /> | 48 <param name="input_files" type="data" format="fasta,fastqsanger,fastqsolexa,fastqillumina" label="Reference(s) input files" /> |
| 40 <section name="lastdb" title="Lastdb arguments" expanded="true"> | 49 <section name="lastdb" title="Lastdb arguments" expanded="true"> |
| 41 <param argument="-Q" type="select" multiple="false" label="Input format"> | |
| 42 <option value="0" selected="true">FASTA</option> | |
| 43 <option value="1">fastq-sanger</option> | |
| 44 <option value="2">fastq-solexa</option> | |
| 45 <option value="3">fastq-illumina</option> | |
| 46 </param> | |
| 47 | |
| 48 <conditional name="sequences_type"> | 50 <conditional name="sequences_type"> |
| 49 <param name="protein" type="select" multiple="false" label="The sequences are :"> | 51 <param name="protein" type="select" multiple="false" label="The sequences are :"> |
| 50 <option value="" selected="true">DNA</option> | 52 <option value="" selected="true">DNA</option> |
| 51 <option value="-p">Proteins (-p)</option> | 53 <option value="-p">Proteins (-p)</option> |
| 52 </param> | 54 </param> |
| 165 <extra_files type="file" value="hedgdb.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/> | 167 <extra_files type="file" value="hedgdb.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/> |
| 166 <extra_files type="file" value="hedgdb.suf" name="lastdb.suf" compare="sim_size" delta="1"/> | 168 <extra_files type="file" value="hedgdb.suf" name="lastdb.suf" compare="sim_size" delta="1"/> |
| 167 <extra_files type="file" value="hedgdb.tis" name="lastdb.tis" compare="sim_size" delta="1"/> | 169 <extra_files type="file" value="hedgdb.tis" name="lastdb.tis" compare="sim_size" delta="1"/> |
| 168 </output> | 170 </output> |
| 169 </test> | 171 </test> |
| 172 <test> | |
| 173 <param name="input_files" value="humanMito.fq" ftype="fastqsanger"/> | |
| 174 <section name="lastdb"> | |
| 175 <param name="Q" value="1"/> | |
| 176 <section name="repeats"> | |
| 177 <param name="uppercase" value="0"/> | |
| 178 <param name="simple_repeat" value="1"/> | |
| 179 <param name="sm_lower" value="true"/> | |
| 180 </section> | |
| 181 </section> | |
| 182 <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb"> | |
| 183 <extra_files type="file" value="humdb-sanger.bck" name="lastdb.bck" compare="sim_size" delta="1"/> | |
| 184 <extra_files type="file" value="humdb-sanger.des" name="lastdb.des"/> | |
| 185 <extra_files type="file" value="humdb-sanger.prj" name="lastdb.prj" lines_diff="1"/> | |
| 186 <extra_files type="file" value="humdb-sanger.sds" name="lastdb.sds"/> | |
| 187 <extra_files type="file" value="humdb-sanger.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/> | |
| 188 <extra_files type="file" value="humdb-sanger.suf" name="lastdb.suf" compare="sim_size" delta="1"/> | |
| 189 <extra_files type="file" value="humdb-sanger.tis" name="lastdb.tis" compare="sim_size" delta="1"/> | |
| 190 </output> | |
| 191 </test> | |
| 170 </tests> | 192 </tests> |
| 171 | 193 |
| 172 <help>@LAST_HELP@</help> | 194 <help>@LAST_HELP@</help> |
| 173 <citations><expand macro="citations"/></citations> | 195 <citations><expand macro="citations"/></citations> |
| 174 </tool> | 196 </tool> |