Mercurial > repos > mvdbeek > get_reference_fasta

changeset 0:b5c0b28cdfb3 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
author mvdbeek
date Thu, 25 Feb 2016 07:19:45 -0500
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files get_reference_fasta.xml test-data/EcR_USP_224.fa test-data/all_fasta.loc tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 6 files changed, 162 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_reference_fasta.xml	Thu Feb 25 07:19:45 2016 -0500
@@ -0,0 +1,29 @@
+<tool id="get_fasta_reference" name="get fasta reference"  version="0.1.1">
+<description>Obtain reference genome sequence</description>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        cat "$pre_installed_fasta.fields.path" > "$output"
+    ]]></command>
+    <inputs>
+          <param help="if you wish to have your fasta sequence listed contact instance administrator" label="Select a fasta sequence" name="pre_installed_fasta" type="select">
+          <options from_data_table="all_fasta"/>
+          </param>
+    </inputs>
+    <outputs>
+        <data name="output" label="${pre_installed_fasta.value_label}" format="fasta" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="pre_installed_fasta" value="EcR_USP_224.fa"/>
+            <output name="output" file="EcR_USP_224.fa"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Places the reference genome sequence in the current history.    
+Useful for sharing purposes or tools that work directly on fasta files.
+
+    ]]></help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/EcR_USP_224.fa	Thu Feb 25 07:19:45 2016 -0500
@@ -0,0 +1,101 @@
+>3L:3245372,3251371
+AGGAGGCTATGTTTCTTAATGATGAACTGGTATATTATATTTTCGAAACTTTCATTTAAT
+GTAAAAACACTGTTATTAGTAAATGGAATCTTCCATAACAGGGTCCACCCCAATCGATCA
+TCCCACTCATTAGGTTTCTTCCTCGTCTGAGAGGACCAGAGGTCCCGAGGCTTGCGTTTT
+TGCGGTGACTGTGGCGTCTGCTGGGTGTCAACATTTAGCCGCATGTTGTGCGGCTGCCAC
+AACTGCAGTTCCCCAATTCTGGATAAAAAAAAAAAAACGCCGTCAAACAGAAGGGTGAAA
+TTAACTTCGGAGTCGGACGAGGAGGAGTGCTTAGCACCCGCATCCAGGCACATGTGCTGT
+TCTTCTCGACATGCGACATTCGTACAGTCGCCGAGTCAATCAGACCGGAAAATATGCACA
+AATTCCAATGGCTTTTGTCATGTTGCAAGGCGATTGTGACTACATTTTTGCCATTTCTAT
+TTCCCAAATAGCGGCTAAAACAGTTGTGGCCATTAACTTAGTGCTATGAATGTAGTTACT
+GTTCTTGTGAATTGCTTAATTTCCCTTTCAATCATCTAAAATAAATAAATACAAATGAAT
+GAACCAAAGTCATTACCCTGCCTAAAACACATTTTCTTCCCTTAGAACTTTGTACCCCTT
+TTATATTTCGAATTGCAAATGGAAGGGTGAAATTAGCGGCAAGTGGAGCTATTTTCCGCG
+CGGTGTATGGTTATCACAACGCTTATCTCACTACGCGATTGTCGGAACCTGTAAACGCGA
+TTTTGTCAGCCAGGTTTTTTTGGCTGCCAGCACTTGACGTGTGTTAAATTAGCATTAAAC
+AATAATTTTGTGCCTGTTTTTCTTTTTTTGGCTTTGCCGCTGTTGTTGTTGCTGTTACTG
+TTGTGGTGAATGCAAAATAAATTGCGCATAAAGTTTAATCACTTTGACTTTGCACAACAC
+ACACGCACGCACACACACTTGCAATGCCAAAAAATAAAAACGCACAACAAAAGATTCTCC
+ACACACAGATACACAGATACTGAATACAATATCGGCAGCAGCAGCGCAAACCAAAACAAC
+AACGACGAGCCCAGTGGACAGTGCAAAATAAGTATAAAAATAAATAAGAAAAATTAAAAA
+AAAAGGAAATAAATAAAAAAATACACAAGGCGAAGGCGACGATGGCAACAGGCAGAGCGA
+GCGGGATGCAAATAGAGTCAACAACCTCCAGTGCATTACTCACTTTTAAAGACCGTGTCT
+GTCCTTCAACGAAAACTTTATCTCTGTCCCTCACTCGCTCGCTCTGCATCTGCATCTCAG
+CTTTTGCTCCCTCTCTCTCTCGCTCGCTCTCACTCGAGCAGCCCGATTCGTTTTTTACTT
+CTTATAATTAAACAATTTTGCAGCGGCACTCCCCCAGCGCCCCCATTTCGTACTCCCCCC
+GCCGTCTTCATCTTTTTCCGGACAAACAGAACCCGAAAAAGTGATCTTGCTGCACGGAAA
+GAAATCGAATCGTTGTCTAACAATAGAAATGCTGCTTTATAAGGCAACCAATTGAAGTCT
+TTCGTTCTTCAAAACCTAATTCAAAGATTAACCACTTTTTTGCTATATCTATCCTTAAGC
+TTTAAAATTCGAATAGTAATAGGATTTAACTCTATAGTAGTAGTATCTTATCATATTATC
+AGTACGATTTTTCCCAAAGTGCCATTGTTTTTGGTCACTATGGTCTTGTTCTTGTTCCCG
+GAGATTTGCACAAGTGTGCAGAAGACAGTCTTCTATCTCCACTTTATCGATGGGGCTTCG
+GAAAGTTTGTCGATTCCGCTGCTGCGCATTTTGGCGAGATGCGAGATGAATAAACTGTTG
+TACGCTTGCGTGACCTGTTCGCCATCTCGGTTGCTCCTCCTGCGCCCTCTTTTCCTCTCT
+CTACCCCCCTCCCCCACGCAAAGGAAAGAGACGGAGCGATTGCCACATCCGCCCTGCATG
+TTTGTGCGCTTTTTGTGCGACTAATGTCATTGACTGCAATTTGTTAGCAAAGTATTTCGA
+CTGATAAACAAAATCTGCACGATGCCAATGAACCCGGCTCTCTAAAATTGCCATCCGAAA
+GCCAAAACAACCCGAAATTGCAATTCGCGCCCCAATTGGAGAGCAACTAGGTAGGCGTGT
+GTAACAGAGATAGCAATCGGGCCTTGCACTCACACTCCCTAAGGAGCAGAGGTGGATTCT
+AACGGGGATTTGACGGAACGCGAATTCTTTAGCATTCTATATCTGCACCTTATAAGAATT
+TCCACTGAGTTCTAAGTTGAGATTTCATAATATTTAGTATTTTAACTATGTTTTTTCGTA
+TAAGTTTTGTTATTACTCTGCTATGACTTCCATAACCCCTTTTTAGAAGTGCTTTTCCTT
+ATCCGCCTCTGCACATGAGCACAGGTTGGCAATGCCATAAACAAAGAATTCCTTTTGTTT
+GTTGATTCGATTTTTGTTCTGCGATCTTTTTATTTCTTTGCAAATTGTATTTTTATTTTT
+AAATAAACAAGCCGAGTTCATTGCATTCGCCAGAATAAGAATATAACAAATACGGCACGA
+AAAGCACTCGACAACCGACAAAAGGCGCAGAAAAACAGGAACGTCGACTGACATACATGG
+CGTATAATTAACGGCTGCGCGTGTAGAGAGAGTTCAAGTTACTTTATCAATTCTTTCTTT
+TTCGGGACCTAACAATACTCATACTTGCACTTAAGTAGGCGGAGTGAAAGCCAAGTCATA
+ATTTCGACGATGCGTATACATATATAGAATCAATCAACTGATTAATTGCAGCTGTGCAAC
+GCTTGAGTTTTTGCCTCAGCCTTTCGTCTGGTGACATAGTTTACTCGATTAATTATGGTA
+AGTAATAAGGGTTTAAAATAATTGAAAACCCCAGCACTTGCGTGTATTATATATAACGAT
+GATTTAACAGCACCTCCTTTATAAATAAAACCAATCCCTTCAAGTGCGAACAGCTATGTT
+TTCCGCTCATCTGGCGCATTTATCAGATGGTGCCATATTTCCTCGGAGAAGAAGGCATTG
+AATGTCAGTGGTGTTCGGATTACACTAAAGTCGGTCAATAACTTCGGACCCCTGCACAAA
+GCGTTTAAGTGACCACAAGTGATCGAGATGTTCCTCTTGTTGTTTACCCCCTTGCCAACT
+GATCTTAAGTTTGGGATGCCACGCTAGTTTAGTTGACCGGTTTAATGACTCGAACTTAAT
+TTGCGCCCTCGGAGAGAGGAAAGTAGCCAGCAAAAAATGCAAGCCGAAAAATATGCGAAA
+CAACCAGGCAGACAACACCCAACGGCAAAAACTCGGCCTGGAGAGAAAGAGGCAGTGGCA
+GCGACGCGTCTGGGGGCTTACAATGGCGGTCGCAACACTAGTGGCGCTTGTAAATAGAGA
+CATAACGAAAAGGTATTAAAAATGATGCGGCAAAAGAAATAACTGCACTATTTTCCATAA
+AAATATTTTGAAAAATAAACTGTTGCGCCGTTTTTAGAGATCTTAAAAACCTCTTTACGT
+CAACTTTGATAACTAATTGAGTTCCTTTGCATAGTTATGATTTTTAAAAATAACAATTTA
+AGATACATGATATTCCCTACATGAACAATTAGTGGTTTATAATAAATAAGCAACCTAATG
+CGTAAGATCCCACAATCTTGACCGCTACTGTGAAAAGGGGGGGATCTGCGTGAGTGTGCG
+TGTATGTGGGGAGAGGGCTGCAGTGGGCGGGGCAGGCTGCAGGAAGAGCCCCCAGGCGAG
+CGTGTGTATGTGAGTGGGTCGCCAAAACAGACAAAAAACGAGGAGTGCATACGAGCAGAA
+GCAGCAGTGCTGCCCCAAAAGAACGATGCTCGAACCGAAAGTAACTCATATTCGCGGCTG
+CGAGAGTGTGTGCGTGTGCGGCGACGGATCAGGCAAATATATAAAGCGGCGATCGGGCAA
+TGCAAACTGCTCATTCCGTCGCCGTTCGTTCCGTTCGCTTTACTTTTCGTACTTTTCTCG
+CATATTAAAAAGTCAAACAAAATAATAAAATGAAGCGATCGCACACATACTCACGCACAT
+ACGTGTATATGTTCGTACATATATATATGTACATATGCATACATATATATGCACGCAATG
+GCCGCCATTGACGCCGACTGCGCTGCCGACTGCGCTGGCGAGAGTATAAAAGCATAAAAT
+CACTTCGTACTCGGGTTTATTAAAACCAAAACTGTGCAAGTGTCAAGATCGGTTAGCAGC
+AGCAAAAAGATAAATAAGAAATAGCCAAGGACCCATAAAATAAATAATCTCAATACCAAA
+AAGTTCTAGTGAAATTCACAATTCTGACTTGGAAAGTGAAAGTTTGGCCATTAAACGTAC
+GATTAAAATCCACAACAGCACGATCAAAAATAGTATCAAGCAATTAGCGCAGAAAAAGTA
+ACAAAAAAAATTTTAAAAAACAGGAACGCGACGTGCCCGCAAAAGCGAAAAAAAATTAAA
+ATCGAAAGTGTTCTACTGACATGGATTACTTTTTGCCGCCCAAACTACAAACACAACAAA
+ACGCGCAGAGAAACTAGCACTACTTTTTTCTATTCACCCATTCGGAGAGTGAGAAGAATC
+GGAGAGAAGGAAAGAGAGCAAAGGCCGGTCCGAAATAGAAAGCACTACACTGGAAAATCT
+GTTAATAAGAATGCAATGAAAGTAATACGAAACACAGATATATTTAGCTTATATTACTCT
+TAAAACTCTAGAAAAATCTAGATCGGTTAATATAACAATTTTAAAATAGCTTAGTTGGCA
+TCGATGTTACGGAAAAAATTTTTCCAGTTGTACTTGAAAGGCAGAAATATTTCGAGATTT
+AGATTTATGAGTCTTCCTAAAGAAATTAAATTGGATAGAAAATGTCTTTTAGATATAGAA
+TACAGGGTGATGCCTAATCCATTAAAATCGAGCAATCTAAAAAGTGTCATACCAGTTAGA
+TTGGGTGTAACCAACGCAACGTTCTCACTGTGTAGATAGCGATCTCTTCTATTCGGCGGT
+GTACGTGCACTTGGCCATTTGTCTCTCCATTCTCCATTTTTCGCGCCTCGCTCTCAATTC
+TCTGCGCTCAAATCCTCTAGCAATTCTAATTCGTATTCTCGCCGCCTCGCTTTGAACTTG
+AACTTTAAATGCACAAACCATAATCGTGTATGTTATGTTGTTGCTGGCCGAGGGCGTGCT
+CTCGCACTCTGGCAAACATGGGCTCTACGAGTTTGCTATATATACGCAGCGCAATCAGTT
+GCGAGGCAGCACTCGTTCCATGTGGGCGCTCGACAATCGCCCGCTGATCAGTTTTCGACT
+GGCTTGCAATTAATTCGGCTCTTGACGAGCCCCAAAAGTGAAAGTCGCGAGTGAAAGACG
+TGGCAGTTTTATATTAAAGAAAAATACGAAAACGGGCAGCAGATCAAACATGAACAGTAC
+GCAAAACACGAAATGCGAAACGGCGGCAACAAGTTAATAAATTAAGACGGCAAACGAAAA
+AATCCAGATTCCGAGCACTGCAAAGAAAGTGGCACAAATGCTTTGCTTTTATCGTAGGAA
+ATTCGCAAAAAATGTACAAATAAAACGAAAGAAAAGTTGCCACTATCAAATCCCACCGTT
+CTTTAACTATAGTTTCCTTCTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCGAAA
+GCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGAACAATCAGCGAAAACG
+GAATCGATTACAGTTTTGGAGATCGTGAGAGGAGGAGAAGAGGCGACTGCTTGATAAGCC
+CGGACCCTCCAGCGATCTCCAATCAATATTACTTTCCACCTACATATCTCCCCCTTTCAG
+CTGGTTTAATTTTGGATTCCCCCATCTGGCTGGCCTATTTTCGCCTGGCCTGCGTTATTT
+ATTAGTTAATAAACCATTAATATATACTTGAATAAAAAGGCGTTTCTCTGATTTTTGATG
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc	Thu Feb 25 07:19:45 2016 -0500
@@ -0,0 +1,1 @@
+EcR_USP_224.fa	EcR_USP_224.fa	EcR_USP_224.fa	${__HERE__}/EcR_USP_224.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Thu Feb 25 07:19:45 2016 -0500
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>		<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3		/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Feb 25 07:19:45 2016 -0500
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Thu Feb 25 07:19:45 2016 -0500
@@ -0,0 +1,6 @@
+<tables>
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_fasta.loc" />
+    </table>
+</tables>