# HG changeset patch
# User cpt
# Date 1726634676 0
# Node ID 0f6659efd912abf07e3b7ae127c8b1cc95b4b833
# Parent  bc16792ecfd2ae68ec86de264b67e5a66193fbe7
planemo upload commit d213efcbada7995b34f93ed64202e551fa4fcf07

diff -r bc16792ecfd2 -r 0f6659efd912 generate-putative-isp.xml
--- a/generate-putative-isp.xml	Wed Sep 18 04:25:38 2024 +0000
+++ b/generate-putative-isp.xml	Wed Sep 18 04:44:36 2024 +0000
@@ -5,29 +5,29 @@
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="2019.06.08">regex</requirement>
+        <requirement type="package" version="1.77">biopython</requirement>
     </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>