Mercurial > repos > petr-novak > dante

changeset 24:df99812ded92 draft

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"planemo upload commit a0a9b02c60a91942a271b8b35648c0b152fe1ebd-dirty"
author petr-novak
date Fri, 27 Jan 2023 08:15:31 +0000
parents e2bbc79f0fac
children 74babe57d739
files dante.xml dante_gff_output_filtering.xml dante_gff_to_dna.xml dante_gff_to_tabular.xml summarize_gff.xml
diffstat 5 files changed, 11 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/dante.xml	Wed Jan 25 13:06:55 2023 +0000
+++ b/dante.xml	Fri Jan 27 08:15:31 2023 +0000
@@ -1,7 +1,7 @@
-<tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="1.1.4">
+<tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="1.1.5">
   <description> Tool for annotation of transposable elements based on the similarity to conserved protein domains database. </description>
   <requirements>
-    <requirement type="package">dante=0.1.4</requirement>
+    <requirement type="package">dante=0.1.5</requirement>
   </requirements>
   <stdio>
     <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
@@ -17,12 +17,10 @@
     #end if
     &amp;&amp;
 
-
     dante --query \${INPUT_SEQUENCES} --domain_gff ${DomGff}
 	  --database $database
       --scoring_matrix ${scoring_matrix}
-
-    &amp;&amp;
+      --cpu \${GALAXY_SLOTS:-1}
     dante_gff_output_filtering.py --dom_gff ${DomGff}
     --domains_prot_seq ${Domains_filtered} --domains_filtered ${DomGff_filtered}
     --output_dir .
--- a/dante_gff_output_filtering.xml	Wed Jan 25 13:06:55 2023 +0000
+++ b/dante_gff_output_filtering.xml	Fri Jan 27 08:15:31 2023 +0000
@@ -1,7 +1,7 @@
-<tool id="domains_filter" name="Protein Domains Filter" version="1.1.4">
+<tool id="domains_filter" name="Protein Domains Filter" version="1.1.5">
   <description> Tool for filtering of gff3 output from DANTE. Filtering can be performed based domain type and alignment quality. </description>
     <requirements>
-        <requirement type="package">dante=0.1.4</requirement>
+        <requirement type="package">dante=0.1.5</requirement>
     </requirements>
     <stdio>
         <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
--- a/dante_gff_to_dna.xml	Wed Jan 25 13:06:55 2023 +0000
+++ b/dante_gff_to_dna.xml	Fri Jan 27 08:15:31 2023 +0000
@@ -1,7 +1,7 @@
-<tool id="domains_extract" name="Extract Domains Nucleotide Sequences" version="1.1.4">
+<tool id="domains_extract" name="Extract Domains Nucleotide Sequences" version="1.1.5">
   <description> Tool to extract nucleotide sequences of protein domains found by DANTE </description>
   <requirements>
-    <requirement type="package">dante=0.1.4</requirement>
+    <requirement type="package">dante=0.1.5</requirement>
   </requirements>
   <command>
     TEMP_DIR_LINEAGES=\$(mktemp -d) &amp;&amp;
--- a/dante_gff_to_tabular.xml	Wed Jan 25 13:06:55 2023 +0000
+++ b/dante_gff_to_tabular.xml	Fri Jan 27 08:15:31 2023 +0000
@@ -1,6 +1,6 @@
-<tool id="gff_to_tabular" name="Convert dante gff3 to tab delimited file" version="0.1.4" python_template_version="3.5">
+<tool id="gff_to_tabular" name="Convert dante gff3 to tab delimited file" version="0.1.5" python_template_version="3.5">
     <requirements>
-        <requirement type="package">dante=0.1.4</requirement>
+        <requirement type="package">dante=0.1.5</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         summarize_gff.R '$inputgff' '$output'
--- a/summarize_gff.xml	Wed Jan 25 13:06:55 2023 +0000
+++ b/summarize_gff.xml	Fri Jan 27 08:15:31 2023 +0000
@@ -1,6 +1,6 @@
-<tool id="gff_summary" name="Summarize gff3 output from DANTE" version="0.1.4" python_template_version="3.5">
+<tool id="gff_summary" name="Summarize gff3 output from DANTE" version="0.1.5" python_template_version="3.5">
     <requirements>
-        <requirement type="package">dante=0.1.4</requirement>
+        <requirement type="package">dante=0.1.5</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         summarize_gff.R '$inputgff' '$output' '$group'