Mercurial > repos > cpt > cpt_putative_isp

changeset 7:f0ca7edbe202 draft

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planemo upload commit ad5355b899dc8f8300c206522e2a65d49809fb73
author cpt
date Fri, 20 Sep 2024 02:35:30 +0000
parents 7a0ed74e9ff8
children b5c1b167df3c
files generate-putative-isp.xml
diffstat 1 files changed, 23 insertions(+), 25 deletions(-) [+]
line wrap: on
line diff
--- a/generate-putative-isp.xml	Wed Sep 18 05:03:59 2024 +0000
+++ b/generate-putative-isp.xml	Fri Sep 20 02:35:30 2024 +0000
@@ -3,33 +3,31 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="3.9">python</requirement>
+    <expand macro="requirements">
         <requirement type="package" version="2019.06.08">regex</requirement>
-        <requirement type="package" version="1.77">biopython</requirement>
-        <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
-    </requirements>
+    </expand>
     <command detect_errors="aggressive"><![CDATA[
-    python '$__tool_directory__/generate-putative-isp.py'
-    '$fasta_file'
-    --strand '$strand'
-    --switch '$switch'
-    --isp_on '$isp_on'
-    --isp_op '$isp_op'
-    --isp_ob '$isp_ob'
-    --isp_og '$isp_og'
-    --isp_min_len '$isp_min_len'
-    --isp_min_dist '$isp_min_dist'
-    --isp_max_dist '$isp_max_dist'
-    --min_tmd_size '$min_tmd_size'
-    --max_tmd_size '$max_tmd_size'
-    --putative_isp '$putative_isp'
-    --summary_isp_txt '$summary_isp'
-    --putative_isp_gff '$putative_isp_gff'
-    --isp_max '$isp_max'
-    --peri_min '$peri_min'
-    --peri_max '$peri_max'
-    ]]></command>
+python '$__tool_directory__/generate-putative-isp.py'
+'$fasta_file'
+--strand '$strand'
+--switch '$switch'
+--isp_on '$isp_on'
+--isp_op '$isp_op'
+--isp_ob '$isp_ob'
+--isp_og '$isp_og'
+--isp_min_len '$isp_min_len'
+--isp_min_dist '$isp_min_dist'
+--isp_max_dist '$isp_max_dist'
+--min_tmd_size '$min_tmd_size'
+--max_tmd_size '$max_tmd_size'
+--putative_isp '$putative_isp'
+--summary_isp_txt '$summary_isp'
+--putative_isp_gff '$putative_isp_gff'
+--isp_max '$isp_max'
+--peri_min '$peri_min'
+--peri_max '$peri_max'
+
+]]></command>
     <inputs>
         <param type="select" label="Strand Choice" name="strand">
             <option value="both">both</option>