# HG changeset patch
# User nml
# Date 1662149888 0
# Node ID c60899ab28a00439e93bf743cfedf217c758c5bb

planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3051c6185128618cb9f137a10f45c248f6a6097f

diff -r 000000000000 -r c60899ab28a0 spades_header_fixer.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spades_header_fixer.xml	Fri Sep 02 20:18:08 2022 +0000
@@ -0,0 +1,39 @@
+<tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.2+galaxy0">
+	<description>Fixes Spades Fasta ids</description>
+  <requirements>
+      <requirement type="package" version="4.7.0">sed</requirement>
+  </requirements>
+  <command >sed -r "s/>NODE(_[0-9]+)_(.*)|>contig/>${input.element_identifier}\1 \2/g" $input >$output</command>
+	<inputs>
+		<param name="input" type="data" format="fasta" label="Fix these fasta headers"/>
+		</inputs>
+	<outputs>
+		<data name="output" format="fasta"/>
+	</outputs>
+  <tests>
+    <test>
+         <param name="input" value="spades_before_1.fasta" />
+         <output name="output" file="spades_header_fixed_1.fasta" ftype="fasta"/>
+    </test>
+    <test>
+         <param name="input" value="spades_before_2.fasta" />
+         <output name="output" file="spades_header_fixed_2.fasta" ftype="fasta"/>
+    </test>
+  </tests>
+
+	<help><![CDATA[
+    SPAdes fasta header fixer
+    =======
+
+    The SPAdes header fixer tool replaces the default value of NODE from SPAdes fasta header(s) to either a filename or a collection identifier.
+	]]></help>
+
+  <citations>
+        <citation type="bibtex">@ARTICLE{a1,
+            title = {SPAdes fasta header fixer},
+            author = {Philip Mabon},
+            url = {https://github.com/phac-nml/galaxy_tools}
+            }
+        }</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r c60899ab28a0 test-data/spades_before_1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/spades_before_1.fasta	Fri Sep 02 20:18:08 2022 +0000
@@ -0,0 +1,15 @@
+>NODE_1_length_792_cov_31.561498
+TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTG
+TCGCTCCAGCATTACTGGAACGGGCGCTAATGTAGGGAAATATCTTTTCTACGTCAATCA
+ACTTTTTTAAAAAAAAGCGCGTTTATACAAACTTCCACCAATCTGTGGTTTTAATAAGCG
+AAAACTGCTTTTTTTGCCCGCGCCGGGAAATTTGCTATGCTGCACATCCCGTTGAAAACG
+CTGATAACAGGCGCAATCACATTCCGCACAATACTGCTCAGGAGATAACATGGAGATAAT
+TTTTTATCACCCGACATTTAACACCGCCTGGTGGGTAAATGCGCTGGAGAAGGCTCTCCC
+ACATGCGCGCGTTCGTGAATGGAAGGTCGGTGATAACAACCCCGCAGACTATGCGCTTGT
+ATGGCAGCCCCCGGTTGAAATGCTGGCCGGAAGACGCTTAAAAGCCGTCTTTGCGCTGGG
+CGCGGGGGTGGATGCAATTCTGAGTAAATTAAATGCGCATCCGGAAATGCTGGACGCCTC
+CATTCCTCTATTCCGTCTGGAAGATACCGGAATGGGCCTGCAAATGCAGGAATATGCCGT
+AAGTCAGGTATTACACTGGTTCCGTCGTTTCGATGATTATCAGGCGCTGAAAAATCAGGC
+GCTATGGAAACCGTTGCCGGAATATACCCGCGAAGAGTTTAGCGTCGGTATCATGGGCGC
+AGGGGTACTGGGCGCAAAAGTGGCAGAAAGTCTACAGGCGTGGGGGTTCCCGTTACGTTG
+
diff -r 000000000000 -r c60899ab28a0 test-data/spades_before_2.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/spades_before_2.fasta	Fri Sep 02 20:18:08 2022 +0000
@@ -0,0 +1,15 @@
+>contig00001 len=272039 cov=11.6 corr=0 origname=NODE_1_length_272039_cov_11.639952 sw=shovill-spades/1.0.4 date=20211013
+TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTG
+TCGCTCCAGCATTACTGGAACGGGCGCTAATGTAGGGAAATATCTTTTCTACGTCAATCA
+ACTTTTTTAAAAAAAAGCGCGTTTATACAAACTTCCACCAATCTGTGGTTTTAATAAGCG
+AAAACTGCTTTTTTTGCCCGCGCCGGGAAATTTGCTATGCTGCACATCCCGTTGAAAACG
+CTGATAACAGGCGCAATCACATTCCGCACAATACTGCTCAGGAGATAACATGGAGATAAT
+TTTTTATCACCCGACATTTAACACCGCCTGGTGGGTAAATGCGCTGGAGAAGGCTCTCCC
+ACATGCGCGCGTTCGTGAATGGAAGGTCGGTGATAACAACCCCGCAGACTATGCGCTTGT
+ATGGCAGCCCCCGGTTGAAATGCTGGCCGGAAGACGCTTAAAAGCCGTCTTTGCGCTGGG
+CGCGGGGGTGGATGCAATTCTGAGTAAATTAAATGCGCATCCGGAAATGCTGGACGCCTC
+CATTCCTCTATTCCGTCTGGAAGATACCGGAATGGGCCTGCAAATGCAGGAATATGCCGT
+AAGTCAGGTATTACACTGGTTCCGTCGTTTCGATGATTATCAGGCGCTGAAAAATCAGGC
+GCTATGGAAACCGTTGCCGGAATATACCCGCGAAGAGTTTAGCGTCGGTATCATGGGCGC
+AGGGGTACTGGGCGCAAAAGTGGCAGAAAGTCTACAGGCGTGGGGGTTCCCGTTACGTTG
+
diff -r 000000000000 -r c60899ab28a0 test-data/spades_header_fixed_1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/spades_header_fixed_1.fasta	Fri Sep 02 20:18:08 2022 +0000
@@ -0,0 +1,15 @@
+>spades_before_1.fasta_1 length_792_cov_31.561498
+TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTG
+TCGCTCCAGCATTACTGGAACGGGCGCTAATGTAGGGAAATATCTTTTCTACGTCAATCA
+ACTTTTTTAAAAAAAAGCGCGTTTATACAAACTTCCACCAATCTGTGGTTTTAATAAGCG
+AAAACTGCTTTTTTTGCCCGCGCCGGGAAATTTGCTATGCTGCACATCCCGTTGAAAACG
+CTGATAACAGGCGCAATCACATTCCGCACAATACTGCTCAGGAGATAACATGGAGATAAT
+TTTTTATCACCCGACATTTAACACCGCCTGGTGGGTAAATGCGCTGGAGAAGGCTCTCCC
+ACATGCGCGCGTTCGTGAATGGAAGGTCGGTGATAACAACCCCGCAGACTATGCGCTTGT
+ATGGCAGCCCCCGGTTGAAATGCTGGCCGGAAGACGCTTAAAAGCCGTCTTTGCGCTGGG
+CGCGGGGGTGGATGCAATTCTGAGTAAATTAAATGCGCATCCGGAAATGCTGGACGCCTC
+CATTCCTCTATTCCGTCTGGAAGATACCGGAATGGGCCTGCAAATGCAGGAATATGCCGT
+AAGTCAGGTATTACACTGGTTCCGTCGTTTCGATGATTATCAGGCGCTGAAAAATCAGGC
+GCTATGGAAACCGTTGCCGGAATATACCCGCGAAGAGTTTAGCGTCGGTATCATGGGCGC
+AGGGGTACTGGGCGCAAAAGTGGCAGAAAGTCTACAGGCGTGGGGGTTCCCGTTACGTTG
+
diff -r 000000000000 -r c60899ab28a0 test-data/spades_header_fixed_2.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/spades_header_fixed_2.fasta	Fri Sep 02 20:18:08 2022 +0000
@@ -0,0 +1,15 @@
+>spades_before_2.fasta 00001 len=272039 cov=11.6 corr=0 origname=NODE_1_length_272039_cov_11.639952 sw=shovill-spades/1.0.4 date=20211013
+TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTG
+TCGCTCCAGCATTACTGGAACGGGCGCTAATGTAGGGAAATATCTTTTCTACGTCAATCA
+ACTTTTTTAAAAAAAAGCGCGTTTATACAAACTTCCACCAATCTGTGGTTTTAATAAGCG
+AAAACTGCTTTTTTTGCCCGCGCCGGGAAATTTGCTATGCTGCACATCCCGTTGAAAACG
+CTGATAACAGGCGCAATCACATTCCGCACAATACTGCTCAGGAGATAACATGGAGATAAT
+TTTTTATCACCCGACATTTAACACCGCCTGGTGGGTAAATGCGCTGGAGAAGGCTCTCCC
+ACATGCGCGCGTTCGTGAATGGAAGGTCGGTGATAACAACCCCGCAGACTATGCGCTTGT
+ATGGCAGCCCCCGGTTGAAATGCTGGCCGGAAGACGCTTAAAAGCCGTCTTTGCGCTGGG
+CGCGGGGGTGGATGCAATTCTGAGTAAATTAAATGCGCATCCGGAAATGCTGGACGCCTC
+CATTCCTCTATTCCGTCTGGAAGATACCGGAATGGGCCTGCAAATGCAGGAATATGCCGT
+AAGTCAGGTATTACACTGGTTCCGTCGTTTCGATGATTATCAGGCGCTGAAAAATCAGGC
+GCTATGGAAACCGTTGCCGGAATATACCCGCGAAGAGTTTAGCGTCGGTATCATGGGCGC
+AGGGGTACTGGGCGCAAAAGTGGCAGAAAGTCTACAGGCGTGGGGGTTCCCGTTACGTTG
+