Mercurial > repos > iuc > te_finder

changeset 1:2edb80d68a1b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit 5d19bf766a0ac0121ce45b5c532ea5e43825082b
author iuc
date Fri, 23 Sep 2022 11:00:13 +0000
parents 838fb3a1678f
children
files TEfinder.xml macros.xml
diffstat 2 files changed, 27 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/TEfinder.xml	Mon Aug 08 19:41:18 2022 +0000
+++ b/TEfinder.xml	Fri Sep 23 11:00:13 2022 +0000
@@ -1,14 +1,10 @@
-<tool id="te_finder" name="TEfinder" version="1.0.1" profile="21.05">
+<tool id="te_finder" name="TEfinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <description>Transposable element insertions finder</description>
-
-    <requirements>
-        <requirement type="package" version="1.15.1">samtools</requirement>
-        <requirement type="package" version="2.30.0">bedtools</requirement>
-        <requirement type="package" version="2.27.4">picard</requirement>
-        <requirement type="package" version="3.4">grep</requirement>
-        <requirement type="package" version="1.07.1">bc</requirement>
-    </requirements>
-
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
     <command>
         <![CDATA[
             '$__tool_directory__/TEfinder' -fa '$required_inputs.FastaFile' 
@@ -32,9 +28,9 @@
         <!-- <param format="fasta" name="input" type="data" label="Source file"/> -->
         <section name="required_inputs" title="Required Inputs" expanded="True">
             <param name="FastaFile" type="data" format="fasta" label="Select reference genome FASTA index (FA/FASTA file)" />
-            <param name="alignmentFile" type="data" format="bam" label="Select sample reads aligned to reference genome (BAM/SAM file)" />
-            <param name="TransposonsInGenome" type="data" format="gtf" label="Select reference genome TE annotation (GFF/GTF file)" />
-            <param name="TransposonsToSearch" type="data" format="text" label="Select TE names" help="Single column text file" />
+            <param name="alignmentFile" type="data" format="bam,sam" label="Select sample reads aligned to reference genome (BAM/SAM file)" />
+            <param name="TransposonsInGenome" type="data" format="gtf,gff" label="Select reference genome TE annotation (GFF/GTF file)" />
+            <param name="TransposonsToSearch" type="data" format="txt" label="Select TE names" help="Single column text file" />
         </section>
         <!-- Advanced Options  -->
         <section name="advanced_options" title="Advanced Options" expanded="False">
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Sep 23 11:00:13 2022 +0000
@@ -0,0 +1,18 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.15.1">samtools</requirement>
+            <requirement type="package" version="2.30.0">bedtools</requirement>
+            <requirement type="package" version="2.27.4">picard</requirement>
+            <requirement type="package" version="3.4">grep</requirement>
+            <requirement type="package" version="1.07.1">bc</requirement>
+        </requirements>
+    </xml>
+    <token name="@TOOL_VERSION@">1.0.1</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">tefinder</xref>
+        </xrefs>
+    </xml>
+</macros>