| Previous changeset 17:7799d65f36ea (2018-06-12) Next changeset 19:813f7ef1b1b5 (2018-06-14) |
|
Commit message:
Uploaded |
|
modified:
gene_family_scaffold_updater.xml |
| b |
| diff -r 7799d65f36ea -r f7bfe1fbd543 gene_family_scaffold_updater.xml --- a/gene_family_scaffold_updater.xml Tue Jun 12 08:10:13 2018 -0400 +++ b/gene_family_scaffold_updater.xml Thu Jun 14 14:32:13 2018 -0400 |
| b |
| @@ -7,7 +7,7 @@ <requirement type="package" version="2.7.1">blast</requirement> <requirement type="package" version="3.1b2">hmmer</requirement> <requirement type="package" version="7.313">mafft</requirement> - <requirement type="package" version="5.22.0_0">perl</requirement> + <requirement type="package" version="5.22.0">perl</requirement> <requirement type="package" version="1.641">perl-dbi</requirement> <requirement type="package" version="3.5.3">perl-dbd-pg</requirement> </requirements> @@ -18,23 +18,43 @@ --coding_sequences '$input_coding_sequences' --scaffold '$GALAXY_DATA_INDEX_DIR/plant_tribes/scaffolds/$scaffold' --species_name '$species_name' +--species_code '$species_code' --species_family '$species_family' --species_order '$species_order' --species_group '$species_group' --species_clade '$species_clade' ---rooting_order '$rooting_order_config' +--rooting_order_species_code '$rooting_order_species_code' --num_threads \${GALAXY_SLOTS:-4} &>'$output']]></command> <inputs> <expand macro="param_scaffold"/> - <param name="input_proteins" format="fasta" type="data" optional="false" label="Proteins fasta file"/> - <param name="input_coding_sequences" format="fasta" type="data" optional="false" label="Coding sequences fasta file"/> - <param name="species_name" type="text" optional="false" value="" label="Species name"/> - <param name="species_family" type="text" optional="false" value="" label="Species family"/> - <param name="species_order" type="text" optional="false" value="" label="Species order"/> - <param name="species_group" type="text" optional="false" value="" label="Species group"/> - <param name="species_clade" type="text" optional="false" value="" label="Species clade"/> - <param name="rooting_order_config" format="txt" type="data" optional="false" label="Rooting order config file"/> + <param name="input_proteins" format="fasta" type="data" label="Proteins fasta file"> + <validator type="empty_field"/> + </param> + <param name="input_coding_sequences" format="fasta" type="data" label="Coding sequences fasta file"> + <validator type="empty_field"/> + </param> + <param name="species_name" type="text" value="" label="Species name"> + <validator type="empty_field"/> + </param> + <param name="species_code" type="text" value="" label="Species code"> + <validator type="empty_field"/> + </param> + <param name="species_family" type="text" value="" label="Species family"> + <validator type="empty_field"/> + </param> + <param name="species_order" type="text" value="" label="Species order"> + <validator type="empty_field"/> + </param> + <param name="species_group" type="text" value="" label="Species group"> + <validator type="empty_field"/> + </param> + <param name="species_clade" type="text" value="" label="Species clade"> + <validator type="empty_field"/> + </param> + <param name="rooting_order_species_code" type="text" label="Species code for rooting order" help="The new species above will be placed immediately after this species code in the rooting order configuration file"> + <validator type="empty_field"/> + </param> </inputs> <outputs> <data name="output" format="txt"/> @@ -68,3 +88,4 @@ </citation> </citations> </tool> + |