Mercurial > repos > petr-novak > dante_ltr

changeset 16:7ec262f92d89 draft

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planemo upload commit ba9c740b818bbd5b5a7a5e2afbea827f5bb91419
author petr-novak
date Wed, 10 May 2023 13:07:41 +0000
parents 0ea5d893a057
children d1c3b29b1478
files clean_dante_ltr.xml dante_ltr_search.xml dante_ltr_summary.xml
diffstat 3 files changed, 22 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/clean_dante_ltr.xml	Wed Apr 26 06:01:25 2023 +0000
+++ b/clean_dante_ltr.xml	Wed May 10 13:07:41 2023 +0000
@@ -1,6 +1,6 @@
-<tool id="clean_dante_ltr" name="DANTE_LTR retrotransposons filtering" version="0.2.2.2" python_template_version="3.5">
+<tool id="clean_dante_ltr" name="DANTE_LTR retrotransposons filtering" version="0.2.2.4" python_template_version="3.5">
     <requirements>
-        <requirement type="package">dante_ltr=0.2.2.2</requirement>
+        <requirement type="package" version="0.2.2.4">dante_ltr</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         clean_ltr.R --gff3 '$dante_ltr' --reference_sequence '$reference' --output output --cpu \${GALAXY_SLOTS:-1}
--- a/dante_ltr_search.xml	Wed Apr 26 06:01:25 2023 +0000
+++ b/dante_ltr_search.xml	Wed May 10 13:07:41 2023 +0000
@@ -1,6 +1,6 @@
-<tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.2.2.2" python_template_version="3.5">
+<tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.2.2.4" python_template_version="3.5">
     <requirements>
-        <requirement type="package">dante_ltr=0.2.2.2</requirement>
+        <requirement type="package" version="0.2.2.4">dante_ltr</requirement>
      </requirements>
     <command detect_errors="exit_code"><![CDATA[
         echo \$PATH
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dante_ltr_summary.xml	Wed May 10 13:07:41 2023 +0000
@@ -0,0 +1,18 @@
+<tool id="dante_ltr_summary" name="Summarize DANTE_LTR output" version="0.2.2.4" python_template_version="3.5">
+    <requirements>
+        <requirement type="package" version="0.2.2.4">dante_ltr</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        dante_ltr_summary.R -g '$input1' -o output &&
+        mv output.pdf '$output1'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="gff3" label="GFF3 output from DANTE_LTR" />
+    </inputs>
+    <outputs>
+        <data label="DANTE_LTR summmary from dataset $input1.hid" format="pdf" name="output1" />
+    </outputs>
+    <help><![CDATA[
+        This tool takes GFF3 output from DANTE_LTR and make graphical summary of the results.
+    ]]></help>
+</tool>