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Changeset 5:b7cf9b172cfe (2016-08-03)

Previous changeset 4:63df1e23f4ff (2016-07-28) Next changeset 6:4d16cf9414cf (2017-02-24)

Commit message:
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b97b90c692604239ed6e9423655c6c5d05798b32-dirty

modified:
macros.xml
tool_dependencies.xml
utils_add-read-counts.xml
utils_estimate-energy.xml
utils_extract-boxed-sequences.xml
utils_filter-annotated-entries.xml
utils_filter-by-energy.xml
utils_find-boxes.xml

added:
test-data/test_22.fixed.fa
test-data/test_23.fixed.fa
utils_fix-fasta-headers.xml

diff -r 63df1e23f4ff -r b7cf9b172cfe macros.xml
--- a/macros.xml Thu Jul 28 10:25:37 2016 -0400
+++ b/macros.xml Wed Aug 03 04:54:40 2016 -0400

[

@@ -1,5 +1,5 @@
<macros>
-    <token name="@VERSION@">smf-v1.6-5_utils-v2.0.1</token>
+    <token name="@VERSION@">smf-v1.6-5_utils-v2.1.0</token>

     <xml name="stdio">
         <stdio>
@@ -17,7 +17,7 @@
         <requirement type="package" version="1.9">numpy</requirement>
         <requirement type="package" version="0.8.2.1">pysam</requirement>
         <requirement type="package" version="0.6.1">htseq</requirement>
-        <requirement type="package" version="2.0.1">segmentation-fold-utils</requirement>
+        <requirement type="package" version="2.1.0">segmentation-fold-utils</requirement>
     ]]></token>

     <token name="@REQUIREMENTS_SMF@"><![CDATA[

diff -r 63df1e23f4ff -r b7cf9b172cfe test-data/test_22.fixed.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_22.fixed.fa Wed Aug 03 04:54:40 2016 -0400

@@ -0,0 +1,2 @@
+>C/D-box_snoRNA
+GCUCUGACCGAAAGGCGUGAUGAGC

diff -r 63df1e23f4ff -r b7cf9b172cfe test-data/test_23.fixed.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_23.fixed.fa Wed Aug 03 04:54:40 2016 -0400

@@ -0,0 +1,2 @@
+>Artificial_double_C/D_K-turn_construct
+GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC

diff -r 63df1e23f4ff -r b7cf9b172cfe tool_dependencies.xml
--- a/tool_dependencies.xml Thu Jul 28 10:25:37 2016 -0400
+++ b/tool_dependencies.xml Wed Aug 03 04:54:40 2016 -0400

@@ -1,7 +1,7 @@
<?xml version="1.0"?>
<tool_dependency>
     <package name="segmentation-fold" version="1.6.5">
-        <repository changeset_revision="f448376f428f" name="package_segmentation_fold_1_6_5__utils_2_0_1" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="cb5aabdbde26" name="package_segmentation_fold_1_6_5__utils_2_1_0" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>


@@ -18,7 +18,7 @@
         <repository changeset_revision="fbb72996807d" name="package_htseq_0_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>

-    <package name="segmentation-fold-utils" version="2.0.1">
-        <repository changeset_revision="f448376f428f" name="package_segmentation_fold_1_6_5__utils_2_0_1" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="segmentation-fold-utils" version="2.1.0">
+        <repository changeset_revision="cb5aabdbde26" name="package_segmentation_fold_1_6_5__utils_2_1_0" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
</tool_dependency>

diff -r 63df1e23f4ff -r b7cf9b172cfe utils_add-read-counts.xml
--- a/utils_add-read-counts.xml Thu Jul 28 10:25:37 2016 -0400
+++ b/utils_add-read-counts.xml Wed Aug 03 04:54:40 2016 -0400

@@ -10,7 +10,7 @@
         <requirement type="package" version="1.9">numpy</requirement>
         <requirement type="package" version="0.8.2.1">pysam</requirement>
         <requirement type="package" version="0.6.1">htseq</requirement>
-        <requirement type="package" version="2.0.1">segmentation-fold-utils</requirement>
+        <requirement type="package" version="2.1.0">segmentation-fold-utils</requirement>
     </requirements>
     <expand macro="stdio" />

diff -r 63df1e23f4ff -r b7cf9b172cfe utils_estimate-energy.xml
--- a/utils_estimate-energy.xml Thu Jul 28 10:25:37 2016 -0400
+++ b/utils_estimate-energy.xml Wed Aug 03 04:54:40 2016 -0400

diff -r 63df1e23f4ff -r b7cf9b172cfe utils_extract-boxed-sequences.xml
--- a/utils_extract-boxed-sequences.xml Thu Jul 28 10:25:37 2016 -0400
+++ b/utils_extract-boxed-sequences.xml Wed Aug 03 04:54:40 2016 -0400

diff -r 63df1e23f4ff -r b7cf9b172cfe utils_filter-annotated-entries.xml
--- a/utils_filter-annotated-entries.xml Thu Jul 28 10:25:37 2016 -0400
+++ b/utils_filter-annotated-entries.xml Wed Aug 03 04:54:40 2016 -0400

diff -r 63df1e23f4ff -r b7cf9b172cfe utils_filter-by-energy.xml
--- a/utils_filter-by-energy.xml Thu Jul 28 10:25:37 2016 -0400
+++ b/utils_filter-by-energy.xml Wed Aug 03 04:54:40 2016 -0400

diff -r 63df1e23f4ff -r b7cf9b172cfe utils_find-boxes.xml
--- a/utils_find-boxes.xml Thu Jul 28 10:25:37 2016 -0400
+++ b/utils_find-boxes.xml Wed Aug 03 04:54:40 2016 -0400

diff -r 63df1e23f4ff -r b7cf9b172cfe utils_fix-fasta-headers.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/utils_fix-fasta-headers.xml Wed Aug 03 04:54:40 2016 -0400

[

@@ -0,0 +1,59 @@
+<tool id="smf_utils_fix-fasta-headers" name="fix-fasta-headers" version="@VERSION@-1">
+    <description>Replaces all spaces with underscores in the ">.."-sequence headers of a FASTA file</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <requirements>
+        <requirement type="package" version="2.7.10">python</requirement>
+        <requirement type="package" version="1.9">numpy</requirement>
+        <requirement type="package" version="0.8.2.1">pysam</requirement>
+        <requirement type="package" version="0.6.1">htseq</requirement>
+        <requirement type="package" version="2.1.0">segmentation-fold-utils</requirement>
+    </requirements>
+
+    <expand macro="stdio" />
+
+    <version_command>@VERSION_COMMAND_UTILS@</version_command>
+
+    <command><![CDATA[
+        segmentation-fold-utils
+            fix-fasta-headers
+                '${fasta_input}'
+                '${fasta_output}'
+    ]]></command>
+
+    <inputs>
+        <param name="fasta_input"
+               type="data"
+               format="fasta"
+               argument="-f"
+               label="Fasta file with RNA-sequece" />
+    </inputs>
+
+    <outputs>
+        <data format="fasta"
+              name="fasta_output"
+              label="${tool.name} on ${str($fasta_input.hid) + ': ' + $fasta_input.name}" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="fasta_input" value="test_22.fa" format="fasta" />
+
+            <output name="fasta_output" file="test_22.fixed.fa" />
+        </test>
+        <test>
+            <param name="fasta_input" value="test_23.fa" format="fasta" />
+
+            <output name="fasta_output" file="test_23.fixed.fa" />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+Replaces all spaces with underscores in the ">.."-sequence headers of a FASTA file for compatibility with pysam indexing.
+    ]]></help>
+
+    <expand macro="citations" />
+</tool>