Mercurial > repos > iuc > maker
comparison maker.xml @ 4:5e96efe6e6c6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b"
author | iuc |
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date | Thu, 10 Oct 2019 02:56:46 -0400 |
parents | 96ac930d84fa |
children | 5201ec38c01f |
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3:96ac930d84fa | 4:5e96efe6e6c6 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="maker" name="Maker" profile="16.04" version="@VERSION@"> | 2 <tool id="maker" name="Maker" profile="16.04" version="@VERSION@+galaxy1"> |
3 <description>genome annotation pipeline</description> | 3 <description>genome annotation pipeline</description> |
4 <macros> | 4 <macros> |
5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
123 rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker | 123 rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker |
124 softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering) | 124 softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering) |
125 | 125 |
126 #else if $repeat_masking.repeat_source.source_type == 'library' | 126 #else if $repeat_masking.repeat_source.source_type == 'library' |
127 model_org= # select a model organism for RepBase masking in RepeatMasker | 127 model_org= # select a model organism for RepBase masking in RepeatMasker |
128 rmlib=${repeat_masking.repeat_source.repeatmasker.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker | 128 #if $repeat_masking.repeat_source.rmlib |
129 rmlib=${repeat_masking.repeat_source.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker | |
130 #else | |
131 rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker | |
132 #end if | |
129 | 133 |
130 #if $repeat_masking.repeat_source.repeat_protein | 134 #if $repeat_masking.repeat_source.repeat_protein |
131 repeat_protein=${repeat_masking.repeat_source.repeat_protein} # provide a fasta file of transposable element proteins for RepeatRunner | 135 repeat_protein=${repeat_masking.repeat_source.repeat_protein} # provide a fasta file of transposable element proteins for RepeatRunner |
132 #else | 136 #else |
133 repeat_protein= # provide a fasta file of transposable element proteins for RepeatRunner | 137 repeat_protein= # provide a fasta file of transposable element proteins for RepeatRunner |
430 </when> | 434 </when> |
431 </conditional> | 435 </conditional> |
432 <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/> | 436 <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/> |
433 </when> | 437 </when> |
434 <when value="library"> | 438 <when value="library"> |
439 <param name="rmlib" type="data" format="fasta" label="Transposable element sequences for RepeatRunner" optional="True" /> | |
435 <param name="repeat_protein" type="data" format="fasta" label="Transposable element protein sequences for RepeatRunner" optional="True" /> | 440 <param name="repeat_protein" type="data" format="fasta" label="Transposable element protein sequences for RepeatRunner" optional="True" /> |
436 <param name="rm_gff" type="data" format="fasta" label="Pre-identified repeat elements from an external GFF file" optional="True" /> | 441 <param name="rm_gff" type="data" format="gff" label="Pre-identified repeat elements from an external GFF file" optional="True" /> |
437 <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/> | 442 <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/> |
438 </when> | 443 </when> |
439 <when value="no"/> | 444 <when value="no"/> |
440 </conditional> | 445 </conditional> |
441 </section> | 446 </section> |