diff funannotate_predict.xml @ 9:d46af27fe48a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 9e3708d04faea0f1be4ea8918e859d6f2c7eb31d

--- a/funannotate_predict.xml	Tue Apr 25 18:28:18 2023 +0000
+++ b/funannotate_predict.xml	Wed Jun 26 09:35:26 2024 +0000
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools" />
     <requirements>
         <expand macro="requirements" />
     </requirements>
@@ -28,6 +29,7 @@
 funannotate predict
 --input input/input.fasta
 --out output
+--tmpdir "\${_GALAXY_JOB_TMP_DIR:-/tmp}"
 #if $uglyTestingHack == "true":
     --database `pwd`'/hacked_database'
 #else
@@ -45,6 +47,7 @@
 --SeqAccession '${organism.SeqAccession}'
 --name '${organism.name}'
 --numbering ${organism.numbering}
+--header_length ${header_length}
 
 #if $parameters:
     --parameters '${parameters}'
@@ -253,7 +256,7 @@
                 <validator type="regex" message="Key must consist of alphanumeric characters only, possibly separated by the period character ('.')">^[\w: ]+$</validator>
             </param>
         </section>
-
+        <param argument="--header_length" type="integer" value="16" min="1" label="Maximum length of FASTA headers" help="The NCBI max FASTA header length is 16. Increase if you don't submit to NCBI." />
         <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
             <option value="gbk" selected="true">Annotated genome (genbank)</option>
             <option value="tbl">NCBI tbl annotation file (use for NCBI submission)</option>
@@ -307,7 +310,7 @@
     </outputs>
     <tests>
         <!-- training from scratch -->
-        <test>
+        <test expect_num_outputs="10">
             <param name="input" value="genome_masked.fa" />
             <param name="database" value="2021-07-20-120000" />
             <section name="busco">
@@ -376,7 +379,7 @@
         </test>
 
         <!-- pre-trained augustus -->
-        <test>
+        <test expect_num_outputs="10">
             <param name="input" value="genome_masked.fa" />
             <param name="database" value="2021-07-20-120000" />
             <section name="organism">
@@ -441,7 +444,7 @@
         </test>
 
         <!-- bam and transcripts and proteins -->
-        <test>
+        <test expect_num_outputs="10">
             <param name="input" value="genome_masked.fa" />
             <param name="database" value="2021-07-20-120000" />
             <section name="organism">
@@ -517,7 +520,7 @@
         </test>
 
         <!-- proteins -->
-        <test>
+        <test expect_num_outputs="10">
             <param name="input" value="genome_masked.fa" />
             <param name="database" value="2021-07-20-120000" />
             <section name="organism">