Mercurial > repos > nilesh > rseqc

changeset 11:d7f6b3653d84 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 08:21:45 +0000
parents c63fbdcc0dbe
children 57fad5deeb8e
files FPKM_count.xml RNA_fragment_size.xml RPKM_saturation.xml bam2wig.xml bam_stat.xml clipping_profile.xml deletion_profile.xml geneBody_coverage.xml geneBody_coverage2.xml infer_experiment.xml inner_distance.xml insertion_profile.xml junction_annotation.xml junction_saturation.xml mismatch_profile.xml read_GC.xml read_NVC.xml read_distribution.xml read_duplication.xml read_hexamer.xml read_quality.xml rseqc_macros.xml tin.xml
diffstat 23 files changed, 34 insertions(+), 36 deletions(-) [+]
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line diff
--- a/FPKM_count.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/FPKM_count.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -1,6 +1,6 @@
 <tool id="rseqc_FPKM_count" name="FPKM Count" version="@WRAPPER_VERSION@.1">
     <description>calculates raw read count, FPM, and FPKM for each gene</description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/RNA_fragment_size.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/RNA_fragment_size.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -2,7 +2,7 @@
     <description>
      calculates the fragment size for each gene/transcript
     </description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/RPKM_saturation.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/RPKM_saturation.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -1,6 +1,6 @@
 <tool id="rseqc_RPKM_saturation" name="RPKM Saturation" version="@WRAPPER_VERSION@.1">
     <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/bam2wig.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/bam2wig.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -2,7 +2,7 @@
     <description>
         converts all types of RNA-seq data from .bam to .wig
     </description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/bam_stat.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/bam_stat.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -2,7 +2,7 @@
     <description>
         reads mapping statistics for a provided BAM or SAM file.
     </description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/clipping_profile.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/clipping_profile.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -2,7 +2,7 @@
     <description>
      estimates clipping profile of RNA-seq reads from BAM or SAM file
     </description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/deletion_profile.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/deletion_profile.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -2,7 +2,7 @@
     <description>
      calculates the distributions of deleted nucleotides across reads
     </description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/geneBody_coverage.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/geneBody_coverage.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -1,19 +1,13 @@
 <tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@WRAPPER_VERSION@.3">
-  <description>
-    Read coverage over gene body.
-  </description>
-
-  <macros>
-    <import>rseqc_macros.xml</import>
-  </macros>
-
+    <description>Read coverage over gene body</description>
+    <expand macro="bio_tools"/>
+    <macros>
+        <import>rseqc_macros.xml</import>
+    </macros>
     <expand macro="requirements" />
-
-  <expand macro="stdio" />
-
-  <version_command><![CDATA[geneBody_coverage.py --version]]></version_command>
-
-  <command><![CDATA[
+    <expand macro="stdio" />
+    <version_command><![CDATA[geneBody_coverage.py --version]]></version_command>
+    <command><![CDATA[
     #if str($batch_mode.batch_mode_selector) == "merge":
         #import re
         #set $input_list = []
--- a/geneBody_coverage2.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/geneBody_coverage2.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -2,7 +2,7 @@
     <description>
         Read coverage over gene body
     </description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/infer_experiment.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/infer_experiment.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -1,6 +1,6 @@
 <tool id="rseqc_infer_experiment" name="Infer Experiment" version="@WRAPPER_VERSION@.1">
     <description>speculates how RNA-seq were configured</description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/inner_distance.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/inner_distance.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -1,6 +1,6 @@
 <tool id="rseqc_inner_distance" name="Inner Distance" version="@WRAPPER_VERSION@.1">
     <description>calculate the inner distance (or insert size) between two paired RNA reads</description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/insertion_profile.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/insertion_profile.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -2,7 +2,7 @@
     <description>
      calculates the distribution of inserted nucleotides across reads
     </description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/junction_annotation.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/junction_annotation.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -1,6 +1,6 @@
 <tool id="rseqc_junction_annotation" name="Junction Annotation" version="@WRAPPER_VERSION@.1">
     <description>compares detected splice junctions to reference gene model</description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/junction_saturation.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/junction_saturation.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -1,6 +1,6 @@
 <tool id="rseqc_junction_saturation" name="Junction Saturation" version="@WRAPPER_VERSION@.1">
     <description>detects splice junctions from each subset and compares them to reference gene model</description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/mismatch_profile.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/mismatch_profile.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -2,7 +2,7 @@
     <description>
      calculates the distribution of mismatches across reads
     </description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/read_GC.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/read_GC.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -1,6 +1,6 @@
 <tool id="rseqc_read_GC" name="Read GC" version="@WRAPPER_VERSION@">
     <description>determines GC% and read count</description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/read_NVC.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/read_NVC.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -1,6 +1,6 @@
 <tool id="rseqc_read_NVC" name="Read NVC" version="@WRAPPER_VERSION@">
     <description>to check the nucleotide composition bias</description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/read_distribution.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/read_distribution.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -1,6 +1,6 @@
 <tool id="rseqc_read_distribution" name="Read Distribution" version="@WRAPPER_VERSION@.1">
     <description>calculates how mapped reads were distributed over genome feature</description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/read_duplication.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/read_duplication.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -1,6 +1,6 @@
 <tool id="rseqc_read_duplication" name="Read Duplication" version="@WRAPPER_VERSION@">
     <description>determines reads duplication rate with sequence-based and mapping-based strategies</description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/read_hexamer.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/read_hexamer.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -2,7 +2,7 @@
     <description>
         calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences
     </description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/read_quality.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/read_quality.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -1,6 +1,6 @@
 <tool id="rseqc_read_quality" name="Read Quality" version="@WRAPPER_VERSION@">
     <description>determines Phred quality score</description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
--- a/rseqc_macros.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/rseqc_macros.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -8,7 +8,11 @@
             <yield/>
         </requirements>
     </xml>
-
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">rseqc</xref>
+        </xrefs>
+    </xml>
     <xml name="stdio">
         <stdio>
             <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
--- a/tin.xml	Thu Nov 28 20:46:57 2019 +0000
+++ b/tin.xml	Wed Sep 01 08:21:45 2021 +0000
@@ -2,7 +2,7 @@
     <description>
         evaluates RNA integrity at a transcript level
     </description>
-
+    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>