Mercurial > repos > rnateam > bctools

changeset 56:b0d5cd8e4c6b draft

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fix requirements xml
author rnateam
date Fri, 12 Feb 2016 08:40:52 -0500
parents 4bedd35bcdff
children 537657678b2b
files convert_bc_to_binary_RY.xml coords2clnt.xml extract_aln_ends.xml extract_bcs.xml merge_pcr_duplicates.xml remove_tail.xml rm_spurious_events.xml
diffstat 7 files changed, 25 insertions(+), 39 deletions(-) [+]
line wrap: on
line diff
--- a/convert_bc_to_binary_RY.xml	Fri Feb 12 08:37:33 2016 -0500
+++ b/convert_bc_to_binary_RY.xml	Fri Feb 12 08:40:52 2016 -0500
@@ -1,10 +1,8 @@
 <tool id="convert_bc_to_binary_RY.py" name="Create binary barcodes" version="0.1.0">
   <description>from regular barcodes.</description>
-  <xml name="requirements">
-      <requirements>
-          <requirement type="package" version="1.66">biopython</requirement>
-      </requirements>
-  </xml>
+  <requirements>
+      <requirement type="package" version="1.66">biopython</requirement>
+  </requirements>
   <macros>
     <import>macros.xml</import>
   </macros>
--- a/coords2clnt.xml	Fri Feb 12 08:37:33 2016 -0500
+++ b/coords2clnt.xml	Fri Feb 12 08:40:52 2016 -0500
@@ -1,10 +1,8 @@
 <tool id="coords2clnt.py" name="Get crosslinked nucleotides" version="0.1.0">
   <description>from full alignments</description>
-  <xml name="requirements">
-      <requirements>
-          <requirement type="package" version="0.6.9">pybedtools</requirement>
-      </requirements>
-  </xml>
+  <requirements>
+      <requirement type="package" version="0.6.9">pybedtools</requirement>
+  </requirements>
   <macros>
     <import>macros.xml</import>
   </macros>
--- a/extract_aln_ends.xml	Fri Feb 12 08:37:33 2016 -0500
+++ b/extract_aln_ends.xml	Fri Feb 12 08:40:52 2016 -0500
@@ -1,11 +1,9 @@
 <tool id="extract_aln_ends.py" name="Extract alignment ends." version="0.2.0">
   <description>from SAM or BAM.</description>
-  <xml name="requirements">
-      <requirements>
-          <requirement type="package" version="0.6.9">pybedtools</requirement>
-          <requirement type="package" version="0.8.3">pysam</requirement>
-      </requirements>
-  </xml>
+  <requirements>
+      <requirement type="package" version="0.6.9">pybedtools</requirement>
+      <requirement type="package" version="0.8.3">pysam</requirement>
+  </requirements>
   <macros>
     <import>macros.xml</import>
   </macros>
--- a/extract_bcs.xml	Fri Feb 12 08:37:33 2016 -0500
+++ b/extract_bcs.xml	Fri Feb 12 08:40:52 2016 -0500
@@ -1,10 +1,8 @@
 <tool id="extract_bcs.py" name="Extract barcodes" version="1.0.0">
   <description>using pattern.</description>
-  <xml name="requirements">
-      <requirements>
-          <requirement type="package" version="1.66">biopython</requirement>
-      </requirements>
-  </xml>
+  <requirements>
+      <requirement type="package" version="1.66">biopython</requirement>
+  </requirements>
   <macros>
     <import>macros.xml</import>
   </macros>
--- a/merge_pcr_duplicates.xml	Fri Feb 12 08:37:33 2016 -0500
+++ b/merge_pcr_duplicates.xml	Fri Feb 12 08:40:52 2016 -0500
@@ -1,12 +1,10 @@
 <tool id="merge_pcr_duplicates.py" name="Merge PCR duplicates" version="0.2.0">
   <description>according to random barcode library.</description>
-  <xml name="requirements">
-      <requirements>
-          <requirement type="package" version="4.1.0">gnu_awk</requirement>
-          <requirement type="package" version="8.22">gnu_coreutils</requirement>
-          <requirement type="package" version="1.0.6">datamash</requirement>
-      </requirements>
-  </xml>
+  <requirements>
+      <requirement type="package" version="4.1.0">gnu_awk</requirement>
+      <requirement type="package" version="8.22">gnu_coreutils</requirement>
+      <requirement type="package" version="1.0.6">datamash</requirement>
+  </requirements>
   <macros>
     <import>macros.xml</import>
   </macros>
--- a/remove_tail.xml	Fri Feb 12 08:37:33 2016 -0500
+++ b/remove_tail.xml	Fri Feb 12 08:40:52 2016 -0500
@@ -1,10 +1,8 @@
 <tool id="remove_tail.py" name="Remove 3'-end nts" version="0.1.0">
   <description>from FASTQ</description>
-  <xml name="requirements">
-      <requirements>
-          <requirement type="package" version="1.66">biopython</requirement>
-      </requirements>
-  </xml>
+  <requirements>
+      <requirement type="package" version="1.66">biopython</requirement>
+  </requirements>
   <macros>
     <import>macros.xml</import>
   </macros>
--- a/rm_spurious_events.xml	Fri Feb 12 08:37:33 2016 -0500
+++ b/rm_spurious_events.xml	Fri Feb 12 08:40:52 2016 -0500
@@ -1,11 +1,9 @@
 <tool id="rm_spurious_events.py" name="Remove spurious" version="0.1.0">
   <description>crosslinking events</description>
-  <xml name="requirements">
-      <requirements>
-          <requirement type="package" version="8.22">gnu_coreutils</requirement>
-          <requirement type="package" version="5.18.1">perl</requirement>
-      </requirements>
-  </xml>
+  <requirements>
+      <requirement type="package" version="8.22">gnu_coreutils</requirement>
+      <requirement type="package" version="5.18.1">perl</requirement>
+  </requirements>
   <macros>
     <import>macros.xml</import>
   </macros>