Mercurial > repos > iuc > trimns

changeset 0:30178a68af68 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
author iuc
date Mon, 01 Feb 2021 19:46:34 +0000
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files TrimNs.xml test-data/in.fasta test-data/out.fasta
diffstat 3 files changed, 85 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TrimNs.xml	Mon Feb 01 19:46:34 2021 +0000
@@ -0,0 +1,35 @@
+<tool id="trimns" name="TrimN" version="0.1.0" profile="20.01">
+    <requirements>
+        <requirement type="package" version="1.0">trimns_vgp</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        remove_fake_cut_sites_DNAnexus.py '$fasta_in' step1_out.fasta step1.log
+        && trim_Ns_DNAnexus.py '$fasta_in' step2_out.list
+        && clip_regions_DNAnexus.py step1_out.fasta step2_out.list final_out.fasta
+    ]]></command>
+    <inputs>
+        <param name="fasta_in" type="data" format="fasta" label="Fasta file input" help="Fasta file to trim, and from which to remove Ns and fake cut sites."/>
+    </inputs>
+    <outputs>
+        <data name="trimmed_out" format="fasta" from_work_dir="final_out.fasta" label="${tool.name} on ${on_string}: trimmed fasta file" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta_in" value="in.fasta"/>
+            <output name="trimmed_out" value="out.fasta" ftype="fasta"/>
+        </test>
+    </tests> 
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+TrimNs is part of the VGP pipeline, and is made of a series of python scripts which trim off large stretches of N bases and to
+remove fake cut sites that sometimes get inserted at the end of bionano hybrid scaffolds.
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1101/2020.05.22.110833</citation>
+        <citation type="doi">10.1101/2020.06.30.177956</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/in.fasta	Mon Feb 01 19:46:34 2021 +0000
@@ -0,0 +1,19 @@
+>contig_0000000001 Coverage: 76.176 Length: 1000
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAAT
+TAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCAT
+TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCT
+GGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA
+GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGNNN
+>contig_0000000001 Coverage: 96.648 Length: 1000
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAAT
+TAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCAT
+TAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG
+TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCT
+GGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA
+GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATT
+>contig_0000000001 Coverage: 56.59 Length: 1000
+NNNNTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAAT
+TAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCAT
+TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCT
+GGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA
+GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.fasta	Mon Feb 01 19:46:34 2021 +0000
@@ -0,0 +1,31 @@
+>contig_0000000001 Coverage: 76.176 Length: 1000
+TTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGAT
+AGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCAC
+TAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAA
+CATCCATGAAACGCATTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGC
+GTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCTGGCA
+GTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCA
+AGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCGCCGGTAATGAAAAA
+GGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCC
+TGTTTACGCGCCG
+>contig_0000000001 Coverage: 96.648 Length: 1000
+TTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGAT
+AGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCAC
+TAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAA
+CATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACG
+GTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGTGAT
+TTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCA
+CAACGTTACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATC
+TACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCA
+CATGGTGCTGATGGGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACG
+CAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATT
+>contig_0000000001 Coverage: 56.59 Length: 1000
+TTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGAT
+AGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCAC
+TAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAA
+CATCCATGAAACGCATTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGC
+GTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCTGGCA
+GTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCA
+AGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCGCCGGTAATGAAAAA
+GGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCC
+TGTTTACGCGCCG