Mercurial > repos > gga > chado_feature_load_fasta
comparison feature_load_fasta.xml @ 6:0e2c2d7d080f draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit a1460ea4dbbd5c6ff6576b2d6db8aaa04b0061a7
| author | gga |
|---|---|
| date | Tue, 04 Sep 2018 12:21:09 -0400 |
| parents | 5b482826e065 |
| children | 11b65a23c85d |
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| 5:5b482826e065 | 6:0e2c2d7d080f |
|---|---|
| 23 --re_name '$re_name' | 23 --re_name '$re_name' |
| 24 #end if | 24 #end if |
| 25 #if $re_uniquename: | 25 #if $re_uniquename: |
| 26 --re_uniquename '$re_uniquename' | 26 --re_uniquename '$re_uniquename' |
| 27 #end if | 27 #end if |
| 28 #if $match_on_name: | |
| 29 $match_on_name | |
| 30 #end if | |
| 31 | 28 |
| 32 $update | 29 $match_on_name |
| 30 | |
| 31 $do_update | |
| 33 | 32 |
| 34 #if $ext_db.db: | 33 #if $ext_db.db: |
| 35 --db '${ext_db.db}' | 34 --db '${ext_db.db}' |
| 36 #end if | 35 #end if |
| 37 #if $ext_db.re_db_accession: | 36 #if $ext_db.re_db_accession: |
| 62 <param name="sequence_type" label="Sequence Type" type="text" value="contig" help="this should be a Sequence Ontology term"/> | 61 <param name="sequence_type" label="Sequence Type" type="text" value="contig" help="this should be a Sequence Ontology term"/> |
| 63 | 62 |
| 64 <param name="re_name" label="Name regular expression" argument="re_name" type="text" help="Regular expression to extract the feature name from the fasta sequence id (first capturing group will be used)." optional="true" /> | 63 <param name="re_name" label="Name regular expression" argument="re_name" type="text" help="Regular expression to extract the feature name from the fasta sequence id (first capturing group will be used)." optional="true" /> |
| 65 <param name="re_uniquename" label="Uniquename regular expression" argument="re_uniquename" type="text" help="Regular expression to extract the feature name from the fasta sequence id (first capturing group will be used)." optional="true" /> | 64 <param name="re_uniquename" label="Uniquename regular expression" argument="re_uniquename" type="text" help="Regular expression to extract the feature name from the fasta sequence id (first capturing group will be used)." optional="true" /> |
| 66 <param name="match_on_name" label="Match on name" argument="match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match existing features using their name instead of their uniquename" /> | 65 <param name="match_on_name" label="Match on name" argument="match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match existing features using their name instead of their uniquename" /> |
| 67 <param name="update" label="Update" argument="update" type="boolean" truevalue="--update" falsevalue="" help="Update existing feature with new sequence instead of throwing an error" /> | 66 <param name="do_update" label="Update" argument="update" type="boolean" truevalue="--update" falsevalue="" help="Update existing feature with new sequence instead of throwing an error" /> |
| 68 <conditional name="relationships"> | 67 <conditional name="relationships"> |
| 69 <param name="rel_type" | 68 <param name="rel_type" |
| 70 argument="--rel_type" | 69 argument="--rel_type" |
| 71 type="select" | 70 type="select" |
| 72 label="Relationship type" | 71 label="Relationship type" |