diff glimmer_extract.xml @ 0:49cf6416bd2b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer_extract.xml	Tue Nov 28 10:17:37 2017 -0500
@@ -0,0 +1,120 @@
+<tool id="glimmer_extract" name="Extract sequence regions" version="@WRAPPER_VERSION@">
+    <description>from a genome</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command><![CDATA[
+        extract
+            -t
+            '$seqInput'
+            '$cordInput' > '$output'
+            2> /dev/null
+    ]]></command>
+    <inputs>
+        <param name="seqInput" type="data" format="fasta" label="Genome Sequence"/>
+        <param name="cordInput" type="data" format="tabular" label="Coordinates" help="See Help below"/>
+    </inputs>
+    <outputs>
+        <data format="fasta" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="seqInput" value='streptomyces_Tu6071_genomic.fasta'/>
+            <param name="cordInput" value='coordTest.txt'/>
+            <output name="output" file='extractTestOutput.fasta' compare="sim_size" delta="20"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+**What it does**
+
+	This program reads a genome sequence and a list of coordinates for it and outputs a multi-
+	fasta file of the regions specified by the coordinates.
+
+-----
+
+**Glimmer Overview**
+
+::
+
+**************		**************		**************		**************
+*            *		*	     *		*            *		*            *
+* long-orfs  *  ===>	*   Extract  *	===>	* build-icm  *  ===>	*  glimmer3  *
+*            *		*	     *		*	     *  	*	     *
+**************		**************		**************		**************
+
+-----
+
+**Example**
+
+
+* input ::
+
+	-Genome Sequence
+
+	CELF22B7  C.aenorhabditis elegans (Bristol N2) cosmid F22B7
+	GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
+	GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
+	TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
+	TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
+	GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
+	ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
+	AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
+	CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
+	TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
+	AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
+	GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
+	AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
+	CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
+	AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
+	GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
+	...
+
+	- Coorinates
+
+	00001   40137      52  +2   0.892
+	00002    1319    1095  -3   0.654
+	00003    1555    1391  -2   0.793
+	00004    1953    2066  +3   1.078
+	00005    2045    2146  +2   0.919
+	00006    4463    4759  +2   0.985
+	00007    6785    6582  -3   1.033
+	00008    6862    7020  +1   0.915
+	00009    7300    7488  +1   0.900
+	00010    7463    7570  +2   0.912
+	00011    8399    8527  +2   1.044
+	00012   10652   10545  -3   0.895
+	00013   12170   12066  -3   1.108
+	00014   13891   13748  -2   0.998
+	00015   14157   14044  -1   1.026
+	00016   15285   15410  +3   0.928
+	00017   15829   15704  -2   0.949
+	...
+
+* output::
+
+		>00001  40137 52  len=135
+		ATGACACATTTGCTCGTTGCTTTGACCCACTACGAGGCCAGTATCATGATTTCTAGAAAA
+		ACCCTCTTTTTGACTTCTTCCTCCATGATCCTTGTAGATTTTGAATTTGAAGTTTTTTCT
+		CATTCCAAAACTCTG
+
+		>00002  1319 1095  len=222
+		TTGGCTCGCCGTTTTGGAGTCCGTGCTGGAATGCCTGGCTTCATCTCAAATAAACTTTGT
+		CCGAGTCTAACGATTGTTCCAGGAAATTACCCTAAATACACTAAAGTCAGTCGCCAATTT
+		TCACAAATTTTCATGGAATACGATTCGGATGTTGGAATGATGTCATTGGATGAGGCATTT
+		ATAGATTTGACAGACTATGTGGCAAGTAATACAGAAAAAAGT
+
+		>00003  1555 1391  len=162
+		ATGGAGAATCTTGAGATGAAACTGGAATCATCTAGAGATTTATCAAGAGACTGTGTTTGT
+		ATAGATATGGATGCTTATTTTGCCGCAGTTGAAATGAGAGATAATCCTGCACTGAGAACA
+		GTTCCTATGGCCGTAGGCTCATCGGCAATGCTGGTAAGCACC
+
+		>00004  1953 2066  len=111
+		GTGCGCGAGAAAAAACTACGCGTTAACCGCCAATTTTCACTTCCCCACAGATCTGTCTCG
+		AGATTCTCGAGTCATTTTTCAAGTTTATTTGTTTGTCAGCGGTTGTTTTAT
+		.....
+    ]]></help>
+    <expand macro="citation" />
+</tool>