diff helixer.xml @ 1:7bc75dd0f782 draft

planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/helixer commit e516933a2c3aa6bcd336a0b5c072893fe9019dd9

--- a/helixer.xml	Wed Jun 28 08:39:38 2023 +0000
+++ b/helixer.xml	Mon Sep 25 12:47:12 2023 +0000
@@ -6,16 +6,12 @@
     </macros>
 
     <requirements>
-        <expand macro="requirements" />
+        <expand macro="requirements"/>
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
-        ## Not in $PATH in the docker image
-        ## Manage models with a data manager?
-        /usr/local/bin/fetch_helixer_models.py
 
-        &&
-
+        /usr/local/bin/fetch_helixer_models.py &&
         Helixer.py
         --fasta-path '$input'
         --species '$species'
@@ -31,7 +27,7 @@
         #else:
             --no-overlap
         #end if
-
+        --batch-size $size
         --window-size $post_processing.window_size
         --min-coding-length $post_processing.min_coding_length
         --edge-threshold $post_processing.edge_threshold
@@ -68,7 +64,7 @@
             </sanitizer>
             <validator type="regex">[0-9a-zA-Z_]+</validator>
         </param>
-
+        <param name="size" argument="--batch-size" type="integer" value="8" label="Batch size" help="It may be necessary to reduce it if the GPU runs out of memory" />
         <section name="post_processing" title="Post-processing">
             <param argument="--window-size" type="integer" min="0" value="100" label="Window size" help="This determines the number of bases averaged during the sliding window approach"/>
             <param argument="--edge-threshold" type="float" min="0" max="1" value="0.1" label="Edge threshold" help="This threshold specifies the genic score which defines the start / end boundaries of each candidate region"/>
@@ -82,26 +78,45 @@
         </data>
     </outputs>
     <tests>
-        <!-- Test for land_plant -->
         <test expect_num_outputs="1">
-            <param name="input" value="sequence.fasta"/>
-            <conditional name="lineage">
-                <param name="lineages" value="land_plant"/>
-            </conditional>
-            <output name="output" value="output.gff3" ftype="gff3" lines_diff="2" />
-        </test>
-        <test expect_num_outputs="1">
-            <!-- Test for species -->
+            <!-- Test for species and land_plant-->
             <param name="input" value="sequence.fasta"/>
             <param name="species" value="Arabidopsis"/>
             <conditional name="lineage">
                 <param name="lineages" value="land_plant"/>
             </conditional>
-            <output name="output" value="ouput_species.gff3" ftype="gff3" lines_diff="2" />
+            <param name="size" value="8"/>
+            <output name="output" value="ouput_species.gff3" ftype="gff3" compare="sim_size" delta="100"/>
+        </test>
+        <test expect_num_outputs="1">
+            <!-- Test for vertebrates-->
+            <param name="input" value="sequence.fasta"/>
+            <conditional name="lineage">
+                <param name="lineages" value="vertebrate"/>
+            </conditional>
+            <param name="size" value="8"/>
+            <output name="output" value="vertebrate.gff3" ftype="gff3" lines_diff="2"/>
+        </test>
+        <test expect_num_outputs="1">
+            <!-- Test for invertebrates-->
+            <param name="input" value="sequence.fasta"/>
+            <conditional name="lineage">
+                <param name="lineages" value="invertebrate"/>
+            </conditional>
+            <param name="size" value="8"/>
+            <output name="output" value="invertebrate.gff3" ftype="gff3" lines_diff="2"/>
+        </test>
+        <test expect_num_outputs="1">
+            <!-- Test for fungi-->
+            <param name="input" value="sequence.fasta"/>
+            <conditional name="lineage">
+                <param name="lineages" value="fungi"/>
+            </conditional>
+            <param name="size" value="8"/>
+            <output name="output" value="fungi.gff3" ftype="gff3" lines_diff="2"/>
         </test>
     </tests>
 
-
     <help><![CDATA[
         Helixer_: Gene calling with Deep Neural Networks.