# HG changeset patch
# User petr-novak
# Date 1691670148 0
# Node ID d1c3b29b147893141b477798c710007022887b11
# Parent  7ec262f92d8931abbea5dcd26f6bbf6cc966ccf8
planemo upload commit ce025ba66edc87ff8ced32d5fdb36109f12cebf0-dirty

diff -r 7ec262f92d89 -r d1c3b29b1478 clean_dante_ltr.xml
--- a/clean_dante_ltr.xml	Wed May 10 13:07:41 2023 +0000
+++ b/clean_dante_ltr.xml	Thu Aug 10 12:22:28 2023 +0000
@@ -1,7 +1,8 @@
-<tool id="clean_dante_ltr" name="DANTE_LTR retrotransposons filtering" version="0.2.2.4" python_template_version="3.5">
-    <requirements>
-        <requirement type="package" version="0.2.2.4">dante_ltr</requirement>
-    </requirements>
+<tool id="clean_dante_ltr" name="DANTE_LTR retrotransposons filtering" version="@TOOL_VERSION@" python_template_version="3.5">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         clean_ltr.R --gff3 '$dante_ltr' --reference_sequence '$reference' --output output --cpu \${GALAXY_SLOTS:-1}
         &&
diff -r 7ec262f92d89 -r d1c3b29b1478 dante_ltr_search.xml
--- a/dante_ltr_search.xml	Wed May 10 13:07:41 2023 +0000
+++ b/dante_ltr_search.xml	Thu Aug 10 12:22:28 2023 +0000
@@ -1,7 +1,8 @@
-<tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.2.2.4" python_template_version="3.5">
-    <requirements>
-        <requirement type="package" version="0.2.2.4">dante_ltr</requirement>
-     </requirements>
+<tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="@TOOL_VERSION@" python_template_version="3.5">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         echo \$PATH
         &&
diff -r 7ec262f92d89 -r d1c3b29b1478 dante_ltr_summary.xml
--- a/dante_ltr_summary.xml	Wed May 10 13:07:41 2023 +0000
+++ b/dante_ltr_summary.xml	Thu Aug 10 12:22:28 2023 +0000
@@ -1,9 +1,10 @@
-<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>
+<tool id="dante_ltr_summary" name="Summarize DANTE_LTR output" version="@TOOL_VERSION@" python_template_version="3.5">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        dante_ltr_summary.R -g '$input1' -o output &&
+        dante_ltr_summary -g '$input1' -o output &&
         mv output.pdf '$output1'
     ]]></command>
     <inputs>
@@ -15,4 +16,4 @@
     <help><![CDATA[
         This tool takes GFF3 output from DANTE_LTR and make graphical summary of the results.
     ]]></help>
-</tool>
+</tool>
\ No newline at end of file
diff -r 7ec262f92d89 -r d1c3b29b1478 dante_ltr_to_library.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dante_ltr_to_library.xml	Thu Aug 10 12:22:28 2023 +0000
@@ -0,0 +1,28 @@
+<tool id="dante_ltr_to_library" name="Create representative library from DANTE_LTR output " version="@TOOL_VERSION@" python_template_version="3.5">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        cp '$dante_ltr' dante_ltr.gff3 &&
+        dante_ltr_to_library --gff3 dante_ltr.gff3 --reference_sequence '$reference' --output output --cpu \${GALAXY_SLOTS:-1} --min_coverage 3
+        &&
+        ls -l output
+        &&
+        mv output/mmseqs2/mmseqs_representative_seq_clean.fasta $dante_ltr_library
+    ]]></command>
+    <inputs>
+        <param type="data" name="dante_ltr" format="gff3"
+               label="GFF3 output from DANTE_LTR retrotransposon identification pipeline"/>
+        <param type="data" name="reference" format="fasta" label="Reference sequence matching input GFF3" />
+    </inputs>
+    <outputs>
+        <data name="dante_ltr_library" format="fasta"
+              label="Representative library from DANTE_LTR $dante_ltr.hid on reference $reference.hid"/>
+    </outputs>
+    <help><![CDATA[
+        This tool extract representative sequences from LTR-RT library identified
+         by DANTE_LTR. Resulting library is suitable for RepeatMasker search.
+    ]]></help>
+</tool>
+
diff -r 7ec262f92d89 -r d1c3b29b1478 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Aug 10 12:22:28 2023 +0000
@@ -0,0 +1,9 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.3.3</token>
+    <token name="@REQUIREMENT_VERSION@">0.2.3.3</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@REQUIREMENT_VERSION@">dante_ltr</requirement>
+        </requirements>
+    </xml>
+</macros>
\ No newline at end of file