Mercurial > repos > sanbi-uwc > reduce_by_merge

changeset 0:4599e6256e81 draft

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planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bea01cf35a3cecf25b2c64197736297d88f05fe6
author sanbi-uwc
date Mon, 16 Jan 2017 08:47:24 -0500
parents
children 8d6874efe309
files reduce_by_merge.xml test-data/input1.fasta test-data/input2.fasta test-data/input3.fasta test-data/output1.fasta
diffstat 5 files changed, 102 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reduce_by_merge.xml	Mon Jan 16 08:47:24 2017 -0500
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<tool id="reduce_by_merge" name="Reduce by Merge" version="0.0.1">
+  <description>Concatenate a collection of FASTA datasets into a single FASTA dataset</description>
+  <command detect_errors="aggressive"><![CDATA[
+    cat
+    #for $input in $input_datasets
+      '${input}'
+    #end for
+    > '${output}'
+    ]]>
+  </command>
+  <inputs>
+    <param name="input_datasets" format="fasta" type="data_collection" collection_type="list" label="Input collection of datasets" />
+  </inputs>
+  <outputs>
+    <data name="output" label="Merge ${on_string}" format="fasta"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_datasets">
+        <collection type="list">
+          <element name="input_datasets.input1" value="input1.fasta" />
+          <element name="input_datasets.input2" value="input2.fasta" />
+          <element name="input_datasets.input3" value="input3.fasta" />
+        </collection>
+      </param>
+      <output name="output" value="output1.fasta" />
+    </test>
+  </tests>
+  <help><![CDATA[
+    Merge all elements of the input collection into a single output dataset by concatenating them together.
+    ]]>
+  </help>
+  <citations>
+  </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1.fasta	Mon Jan 16 08:47:24 2017 -0500
@@ -0,0 +1,8 @@
+>Asian_seabass_ONSAT_SB_Concensus_Lenght_170_bp
+CGAAAAATTTAATAATTTAGGGGTCTTGAGCATGGGCGTGGTAAAATGCCCTCGGTAGCG
+CCACCTACATTTTTAAACGGAACAGCCCCTCAAGCCCGTTGCGCCTAAAAATCTGAAAAT
+CTGCACACATATGTAACATCCCATGACGCACCAAAAAGTCTCTTGGAGCCA
+>Asian_seabass_MOSAT_SB_T_34a_satellite_DNA
+TTTGTGACATCACTACATAGTTTGTTGAAAACGTAC
+>Asian_seabass_MOSAT_SB_T_34b_satellite_DNA
+TTTGTGACATCACACATAGTTGTGGGTCAGTAC 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input2.fasta	Mon Jan 16 08:47:24 2017 -0500
@@ -0,0 +1,16 @@
+>Sat_38
+AAAAAATGTCATAGTATAGTATGGCGTCAAAAAACATG
+>Asian_seabass_Sat_217_Consensus_Length_217_bp
+AGTAAACAAGCATTATGGTTGAAACCATAATTTCCTGTCGGGAGAGCCTTTCCCTCTTTT
+GTGCACTGTATGCAATCCCAGAGTGTGAATAAGCGCTTTTCCAGCGTTTTGAGGCTTATT
+CAGCTCAGAATGGCTTAATACTGCACTATCTGACCAGGACAAAGACAAACTAAGAACTCA
+GCCACACGGACATGAAAGTTGTTTTACTTACAATATT
+>Asian_seabass_Sat_217_Consensus_Length_427_bp
+CCAGCGTTTTGAGGCTTATTCAGCTCAGAATGGCTTAATACTGCACTATCTGACCAGGAC
+AAGACAAACTAAGAACTCAACACACTGACATGAAAGTTTCTATATTTCTATTAAAATAAA
+CAAACATTATGGTTGAAACCATAATTTCATTTCGGGAGAGCCTTTCCCTCTTTGTGGCAC
+TGTATGTAATCTGAAGTGTGAATAACGCTTTTCCCGCGTTTGAGGCTTATTCAGCTCAGA
+ATGGCTTAATACTGCACTATCTGACCAGGACAAGACAAACTAAGAACTCAGCCACACGGA
+CATGAAAGTTGTTTACTTTACAATATTAGTAAACAAGCATTATGGTTGAAACCATAATTT
+CCTGTCGGGAAGAGCTTCCCTCTTTTTGTGCACTGTATGCAATCCCAGAGTGTGAATAAG
+CGCTTTT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input3.fasta	Mon Jan 16 08:47:24 2017 -0500
@@ -0,0 +1,9 @@
+>Asian_seabass_Sat_LM_Consensus_Length_453_bp
+CCCAACAAAATAGCACTTACTGCTTTCCAAATTCAAGTCTGTGCCTGTGTTAGGGTAATG
+TTGGTGATAAATTGATGTACTTAGCTTATCCTGTGAAAATGGTGTAAAATGGCAGTCTCC
+ATGTTTGTTGAAGAAACTCACAACCAAGACAACCCCAAAGAGAAGCACTTATGAAGACAG
+AAATCATGAGTGGCTCTTATTGAAGTGATCAGAGTTGGACTCCATTAAGAAAATGGCTTT
+CAATGTAGTCAGTTGCTTTGTCACTTAAAACTGCCCCAACAAGTAGCACTTACTGCAATT
+TGGTAGTCAAAGTCAATGCTCAAGTTAAGGGTAATAGTAGTGACATAATAGAAAAATCTC
+TAAATATATTTGCTGGCAGCTTTAATATACAGAATGAGTGCCATGATGAATTCTTGATAC
+AGAACAGGGACTTCCAAAATCAGCCAACACTAA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output1.fasta	Mon Jan 16 08:47:24 2017 -0500
@@ -0,0 +1,33 @@
+>Asian_seabass_ONSAT_SB_Concensus_Lenght_170_bp
+CGAAAAATTTAATAATTTAGGGGTCTTGAGCATGGGCGTGGTAAAATGCCCTCGGTAGCG
+CCACCTACATTTTTAAACGGAACAGCCCCTCAAGCCCGTTGCGCCTAAAAATCTGAAAAT
+CTGCACACATATGTAACATCCCATGACGCACCAAAAAGTCTCTTGGAGCCA
+>Asian_seabass_MOSAT_SB_T_34a_satellite_DNA
+TTTGTGACATCACTACATAGTTTGTTGAAAACGTAC
+>Asian_seabass_MOSAT_SB_T_34b_satellite_DNA
+TTTGTGACATCACACATAGTTGTGGGTCAGTAC 
+>Sat_38
+AAAAAATGTCATAGTATAGTATGGCGTCAAAAAACATG
+>Asian_seabass_Sat_217_Consensus_Length_217_bp
+AGTAAACAAGCATTATGGTTGAAACCATAATTTCCTGTCGGGAGAGCCTTTCCCTCTTTT
+GTGCACTGTATGCAATCCCAGAGTGTGAATAAGCGCTTTTCCAGCGTTTTGAGGCTTATT
+CAGCTCAGAATGGCTTAATACTGCACTATCTGACCAGGACAAAGACAAACTAAGAACTCA
+GCCACACGGACATGAAAGTTGTTTTACTTACAATATT
+>Asian_seabass_Sat_217_Consensus_Length_427_bp
+CCAGCGTTTTGAGGCTTATTCAGCTCAGAATGGCTTAATACTGCACTATCTGACCAGGAC
+AAGACAAACTAAGAACTCAACACACTGACATGAAAGTTTCTATATTTCTATTAAAATAAA
+CAAACATTATGGTTGAAACCATAATTTCATTTCGGGAGAGCCTTTCCCTCTTTGTGGCAC
+TGTATGTAATCTGAAGTGTGAATAACGCTTTTCCCGCGTTTGAGGCTTATTCAGCTCAGA
+ATGGCTTAATACTGCACTATCTGACCAGGACAAGACAAACTAAGAACTCAGCCACACGGA
+CATGAAAGTTGTTTACTTTACAATATTAGTAAACAAGCATTATGGTTGAAACCATAATTT
+CCTGTCGGGAAGAGCTTCCCTCTTTTTGTGCACTGTATGCAATCCCAGAGTGTGAATAAG
+CGCTTTT
+>Asian_seabass_Sat_LM_Consensus_Length_453_bp
+CCCAACAAAATAGCACTTACTGCTTTCCAAATTCAAGTCTGTGCCTGTGTTAGGGTAATG
+TTGGTGATAAATTGATGTACTTAGCTTATCCTGTGAAAATGGTGTAAAATGGCAGTCTCC
+ATGTTTGTTGAAGAAACTCACAACCAAGACAACCCCAAAGAGAAGCACTTATGAAGACAG
+AAATCATGAGTGGCTCTTATTGAAGTGATCAGAGTTGGACTCCATTAAGAAAATGGCTTT
+CAATGTAGTCAGTTGCTTTGTCACTTAAAACTGCCCCAACAAGTAGCACTTACTGCAATT
+TGGTAGTCAAAGTCAATGCTCAAGTTAAGGGTAATAGTAGTGACATAATAGAAAAATCTC
+TAAATATATTTGCTGGCAGCTTTAATATACAGAATGAGTGCCATGATGAATTCTTGATAC
+AGAACAGGGACTTCCAAAATCAGCCAACACTAA