Mercurial > repos > sanbi-uwc > reduce_by_merge

changeset 1:8d6874efe309 draft default tip

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planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 2021d9f01d69b1844ddfdb1397bf671fe2d51645
author sanbi-uwc
date Thu, 26 Jan 2017 05:25:35 -0500
parents 4599e6256e81
children
files reduce_by_merge.xml test-data/output1.fasta
diffstat 2 files changed, 11 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/reduce_by_merge.xml	Mon Jan 16 08:47:24 2017 -0500
+++ b/reduce_by_merge.xml	Thu Jan 26 05:25:35 2017 -0500
@@ -1,19 +1,18 @@
 <?xml version="1.0" encoding="utf-8" ?>
-<tool id="reduce_by_merge" name="Reduce by Merge" version="0.0.1">
+<tool id="reduce_by_merge" name="Merge FASTA collection" version="0.0.2">
   <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}'
+      awk 'BEGIN {counter=1} /^>.*/ {print ">${input.element_identifier}_" counter; counter = counter + 1}; /^[^>]/ {print}' '${input}' >> '${output}' &&
     #end for
-    > '${output}'
+    true
     ]]>
   </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"/>
+    <data name="output" label="Merge ${on_string}" format="fasta" />
   </outputs>
   <tests>
     <test>
--- a/test-data/output1.fasta	Mon Jan 16 08:47:24 2017 -0500
+++ b/test-data/output1.fasta	Thu Jan 26 05:25:35 2017 -0500
@@ -1,19 +1,19 @@
->Asian_seabass_ONSAT_SB_Concensus_Lenght_170_bp
+>input_datasets.input1_1
 CGAAAAATTTAATAATTTAGGGGTCTTGAGCATGGGCGTGGTAAAATGCCCTCGGTAGCG
 CCACCTACATTTTTAAACGGAACAGCCCCTCAAGCCCGTTGCGCCTAAAAATCTGAAAAT
 CTGCACACATATGTAACATCCCATGACGCACCAAAAAGTCTCTTGGAGCCA
->Asian_seabass_MOSAT_SB_T_34a_satellite_DNA
+>input_datasets.input1_2
 TTTGTGACATCACTACATAGTTTGTTGAAAACGTAC
->Asian_seabass_MOSAT_SB_T_34b_satellite_DNA
+>input_datasets.input1_3
 TTTGTGACATCACACATAGTTGTGGGTCAGTAC 
->Sat_38
+>input_datasets.input2_1
 AAAAAATGTCATAGTATAGTATGGCGTCAAAAAACATG
->Asian_seabass_Sat_217_Consensus_Length_217_bp
+>input_datasets.input2_2
 AGTAAACAAGCATTATGGTTGAAACCATAATTTCCTGTCGGGAGAGCCTTTCCCTCTTTT
 GTGCACTGTATGCAATCCCAGAGTGTGAATAAGCGCTTTTCCAGCGTTTTGAGGCTTATT
 CAGCTCAGAATGGCTTAATACTGCACTATCTGACCAGGACAAAGACAAACTAAGAACTCA
 GCCACACGGACATGAAAGTTGTTTTACTTACAATATT
->Asian_seabass_Sat_217_Consensus_Length_427_bp
+>input_datasets.input2_3
 CCAGCGTTTTGAGGCTTATTCAGCTCAGAATGGCTTAATACTGCACTATCTGACCAGGAC
 AAGACAAACTAAGAACTCAACACACTGACATGAAAGTTTCTATATTTCTATTAAAATAAA
 CAAACATTATGGTTGAAACCATAATTTCATTTCGGGAGAGCCTTTCCCTCTTTGTGGCAC
@@ -22,7 +22,7 @@
 CATGAAAGTTGTTTACTTTACAATATTAGTAAACAAGCATTATGGTTGAAACCATAATTT
 CCTGTCGGGAAGAGCTTCCCTCTTTTTGTGCACTGTATGCAATCCCAGAGTGTGAATAAG
 CGCTTTT
->Asian_seabass_Sat_LM_Consensus_Length_453_bp
+>input_datasets.input3_1
 CCCAACAAAATAGCACTTACTGCTTTCCAAATTCAAGTCTGTGCCTGTGTTAGGGTAATG
 TTGGTGATAAATTGATGTACTTAGCTTATCCTGTGAAAATGGTGTAAAATGGCAGTCTCC
 ATGTTTGTTGAAGAAACTCACAACCAAGACAACCCCAAAGAGAAGCACTTATGAAGACAG