Mercurial > repos > artbio > small_rna_signatures

diff overlapping_reads.xml @ 12:aa5e2c64dff8 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6806c0677e53d52164707faeb36947987f5c500a
author artbio
date Sat, 22 Oct 2022 23:49:52 +0000
parents 8d3ca9652a5b
children 124f404b0fe7
line wrap: on
line diff
--- a/overlapping_reads.xml	Sat Oct 23 22:55:19 2021 +0000
+++ b/overlapping_reads.xml	Sat Oct 22 23:49:52 2022 +0000
@@ -1,16 +1,16 @@
-<tool id="overlapping_reads" name="Get overlapping reads" version="3.3">
+<tool id="overlapping_reads" name="Get overlapping reads" version="3.4.1">
     <description />
     <requirements>
-        <requirement type="package" version="0.16.0.1=py37h45aed0b_3">pysam</requirement>
-        <requirement type="package" version="1.13=h8c37831_0">samtools</requirement>
+        <requirement type="package" version="0.18.0">pysam</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Tool exception" />
     </stdio>
       <command detect_errors="exit_code"><![CDATA[
-        samtools index '$input' &&
+        ln -f -s $input.metadata.bam_index input.bam.bai &&
+        ln -s $input input.bam &&
         python '$__tool_directory__'/overlapping_reads.py
-           --input '$input'
+           --input input.bam
            --minquery '$minquery'
            --maxquery '$maxquery'
            --mintarget '$mintarget'