Mercurial > repos > iuc > maker
comparison maker.xml @ 4:804af884eef0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b"
| author | iuc |
|---|---|
| date | Thu, 10 Oct 2019 02:55:17 -0400 |
| parents | 681e5067048e |
| children | e06aa22b2e64 |
comparison
equal
deleted
inserted
replaced
| 3:681e5067048e | 4:804af884eef0 |
|---|---|
| 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> |