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changeset 0:a44fc617c657 draft

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planemo upload
author yating-l
date Tue, 16 May 2017 14:50:20 -0400
parents
children 4dc4e3d487c4
files fa_to_twobit.xml test-data/KB462401.fa test-data/KB462401.keepversion.2bit test-data/KB462401.masked.2bit test-data/KB462401.unmasked.2bit tool_dependencies.xml ucsc_macros.xml
diffstat 7 files changed, 252 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fa_to_twobit.xml	Tue May 16 14:50:20 2017 -0400
@@ -0,0 +1,59 @@
+<?xml version="1.0"?>
+<tool id="fa_to_twobit" name="faToTwoBit" version="1.0">
+    <description>Converts a FASTA sequence file into a twoBit file</description>
+
+    <macros>
+        <import>ucsc_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements_twobit" />
+
+    <command detect_errors="exit_code">
+<![CDATA[
+    faToTwoBit
+        "${fasta_input}" ${no_mask} ${strip_version} "${twobit_output}"
+]]>
+    </command>
+    <inputs>
+        <param name="fasta_input" type="data" format="fasta" label="FASTA file" />
+
+        <param name="no_mask" type="boolean" checked="true"
+            truevalue="-noMask" falsevalue=""
+            label="Ignore lower-case masking in fa file"
+            help="-noMask" />
+
+        <param name="strip_version" type="boolean" checked="true"
+            truevalue="-stripVersion" falsevalue=""
+            label="Strip off version number after '.' for GenBank accessions"
+            help="-stripVersion" />
+    </inputs>
+    <outputs>
+        <data name="twobit_output" format="twobit" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta_input" value="KB462401.fa" ftype="fasta" />
+            <output name="twobit_output" file="KB462401.unmasked.2bit" />
+        </test>
+        <test>
+            <param name="fasta_input" value="KB462401.fa" ftype="fasta" />
+            <param name="no_mask" value="" />
+            <output name="twobit_output" file="KB462401.masked.2bit" />
+        </test>
+        <test>
+            <param name="fasta_input" value="KB462401.fa" ftype="fasta" />
+            <param name="strip_version" value="" />
+            <output name="twobit_output" file="KB462401.keepversion.2bit" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+faToTwoBit converts a DNA sequence file in FASTA format into a
+`twoBit Sequence Archive <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_.
+
+    ]]></help>
+
+    <expand macro="citations" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/KB462401.fa	Tue May 16 14:50:20 2017 -0400
@@ -0,0 +1,92 @@
+>KB462401.1 Drosophila biarmipes unplaced genomic scaffold scf7180000301495, whole genome shotgun sequence
+TTAATATGAGAAAAGTGCAAGAAAAGTATAACAAGAAAGGAAGTAAACTTCGGCAAGCCGAAGTTTTTAT
+ACCCTTGCAGATATCTGCAAGGATTATTGCTAGCTTCAGTGGTATATGATATAGTCTTAATCAAATTTAT
+TTCGAAATTCAAAACTAATTAAACAATTTTATTTCCAAGCGTAGGAGGTTCAAGGTTAAAAAACCTCAAA
+TATATTTATTTTTTGTTCCGCACCCCGCTGAAACAAACTTGCGCTGCGCTGGAAGCCCAGGAATCTGCAT
+GCCAAGTTTGAATGTTCTATCTCTTATAGTTTCCGAGATCTCAGCGTTCATACGGACAGACAGACGGACA
+TGACTAGATCGACTCGGCTAGTGATCCTGATCATGAATATATATGGGGTCTGAAACGCTTCCTTCTACCT
+TTTACATACTTTCCGACGAAAGTAGCATACTTATATAAGTTTTACTTATTGGTTTATTAACATATTTGGA
+TACAATAACAATAGCCATTTGTAGCATACTTTGTATAATATGTATGTATCGTCCAATCGTGTGCAAATAA
+AATATTCCGGAACCAAAAAGTAAAAAAAACCGTAAAAAAGCATGTAAAAACTAAGTTTTTCTTTTTGTTT
+TATCAATTAATAGGTTAAGGAAGATGGTTAGCCTACCTATTTCGTCATTCTTTTTTATTTGCCATTTCAA
+TATAAAAAATCCAAAATAATCATTATGAATGAAAAAATAATTAAAAAGAACAGCAATAAACATGTTTTTA
+ATAGATTAGATTAGATAATAGAGTTCTTAAATTCACAAGAAGTCAAGGAAACGTATTCTTCTTCATGTCT
+TTATGAAACCAATATCAGAATAAGTAGCCTAGTTCATTTAGTCATATCCGTCGGTCCAAGCGAATGCTAA
+CATCTCCGAAATTATAAAAATAACTAGTTTGGATATGGGTCATGCAGATTCTTACATTTCCTGTACAGCA
+CAAGTTTGTTTCGTCGAAGTGCCACGCCCACTATTTCTTCTAATACGCGAACTCAATCTGTCTGGAGCCC
+AAACTTTTGAATATTGTGTCAACATTTAATTTTGTTTTGAATATCAACATGAGAATTATTCTTGGTGAAT
+ATCTTTATAAAGGTGTGCCAATGGTTTTAACTTGACCATTTATTTAAATTGATTACCTGAGTAAAGGTTA
+TCTTAAATTCGAGGCACTCAACTAAAGCGATCTCCCTTACTTACCCTTAAACTATTAATTGTTATTCTGA
+AAACTTAAATTCGATAGCTAAATGCCTTATTCAAAGTTCTCGTAATGTTATTTTTAACAGAAAGATTCCG
+TAAATATTTATTTTAAGTGACGACCAGATTATCTCGTTAAAGTTCGAGACGTGTAAAACTTTCTGAAAGT
+TTAAGAGCTGAACCAGGGAAGGTCTTCTTTATAGAATCGAAAACACTTTCTTTCACCTATTGCACTATTA
+AGTCAAGAACATATATAGTTTATGGGGTTGGAAACGTTTCCTTTACTGCGTTGCAAGCTTCTGACAGAAA
+TTATAATACCCTCTGCAAAAATAAAAAATTGCGGTTACAGTGTTGCACTATGATAAACACAGTGGGAAGT
+ACGTAAAAACATGGTTACTAAATCGAATCGGTCCGAAAGGTTTCCCTTTTAAGGCCCATACTGCACACTG
+GTGCAAACATATTTTTAAACATCTTTACTTTGTTAAACAAAAACAGAAGTCCCATAATTGCCCATTTATT
+TGGAAATATGTTTAAAATATATTGATATATACATAATACATGAATATTTATTAAAGTTATTTATTTCATA
+TGACTATAGGAATTACATTTAATTTTTGTATTTAATATAGCTTGTGTTACAAGGGGTCCTTTGGAACACG
+CTGTGATCTGAAAATAGTATTTAAATAGTTTATAAATGCATTAGTTAAACAAGAAAGGACGTTGGCTTTG
+GCAAGCCAAAGTTTGTATACCCTTGCAGCTATAAGAAATACTCTATATTAGTAACAGCATGTTAAATTTT
+TAAGGATTGTTCCTGGCTAGTGATGCTGATCAAGAATATATGTACTTTATGTGGTCGGAAACGTGTCGTT
+CACTGCGTTGCAAACTTCTGAATGAAATCATTATACCCTCTGCAGGCGTTTATAAATTTGTACAAATGGT
+ACAGACTCTTCCAAGGGAAGATGCCAAGAGCTAACGAATGATGAAAACGTTAAGAAGTAAAGAAAATTAT
+TTCGCAATACGCATCACTATCACTGAGGATGTCGATATATCGCCAGGCTCGGACCATGATATTTCCTCTA
+ATCGAAATTGCTAAATTTAGACCAAAACAAGAAAGGAAGTTAACTTCGGCAAGCTGAAGTTTGTATACCC
+TTGCAGACATAAGAAATAATAAGCTTTAGTAAATAATTTTTTCATATTATTTCCCACTAATTTCCCGATT
+GCTCCTATGACAGCTATATGATATAGGCGACCGATTTTGATACAATTTAAGTAGAAATTCAGAACTAATT
+AAAAAATTTTATTTCTATGCTTACAAGGTTATATGTTAAAAAACACCGAAGATATAATTTTTTCATATTA
+TTTTACTACTAATTTTCCGATCTTTCATATGGCAGCTATATGATATAGTCGTCCGATTTTGATAAAATTT
+AATTCGAAATTCAGACCTAACTATAAAATGACATTTCCAAGCTTAGAAGGTGATATGTTAAAAAACACCG
+AAGATATAATTTTTTCATATTATTTTAATACTAACTTTCCGATCTTTCATATGGCAGCTATATGATATAG
+TCGTCCGATTTTGATAAAATTTAATTCGAAATTCAGAACTAATTAAAAAATGTTATTTTCAAGCTTAGAA
+GGTGATATGTTAAAAATCACAGAAGATATAATTTTTTCATATTATTTTAATACTAATTTTCCGATCTTTC
+ATATGGCAGCTATATGATATAGTCGTCCGATTTTGATAAAATTTAATTCGAAATTCAGAACTAATTAAAA
+AATGTTATTTTCAAGCTTAGAAGGTGATATGTTAAAAAACAGCGAAGGTATAATTTTTTCATATTATTTT
+AATTCTATTGATATAGTGGTCCGATTTTGATTAAATTTAATTCGAAATTCAGAACTAATTAAAAAATGTC
+ATTTCCAAGCTTAGAAGGTTATATGCTACAAAACACCGAATATATAATTTTTAAAAATTTTTCCCCTATA
+GTTCCAATGGGAGCTATAAAATATAGTTGTCTGATCCGGCTGGTTCCGACTTATATACTACCTGCAATAC
+AAAGAAAACTTTTGGGAAAGTTTCAGCCCGATAGCTTCAGAACTGAGGGACTAGTTTGCGTAGAAACGGA
+CGGCCAGGCGGACGGACAGACGGACATGGCTAGATCGAATCGTCTAGTGACGTTGATTAAGAATGTATAT
+ATTTTATGGGGTCGGAAACGTCTCCTTCACTGCGTTGCAAACTTCTGACTGAAATTATTATACCCTCTGC
+AAGGGTATAATGAACATCACATAAGCACCGCACAAGAACTATTCAATGACGTCAACGACGATCCAGATTT
+ACTCAAAAAAGTCGTAGCTGGTCCCGAATTCTGGGTTTTTGCTTATAATTTCGGTACCAAAGCCCAATCC
+TTCTAACGGAAGAGCACAGATGAGCCAAGACCGAAAAAGCTAACCTTTACGCCTCTAACAACCGAACAAA
+GAATGATATAAACTTGAAACAAGGTACAGGTGTTTTGGAAAAAGTGTACCTATATACCAAACCAAAAAAA
+TTGATAATCGAAAATACGTGGCCCTCGAAGTTTGAAAAGTCACCTTTTTTTTTGAACACACCTCTTAGGT
+ATTCACTAGTCGGCATAATTATATTGACAAAACAAAAGTTAAATATACTCATAAATAAAACTTACTTCTT
+TTAACTTTTGGCATCAATGTAAATGTAATTTAAATGCTTGAACGCTTGCACTATACAATACGTATTCATT
+CAGTACTTATTGAAAAAGACGAATTTATGTTAGAATCTACTTTTAAGACTTTTTTCCTCGCCTTGAAAAC
+TTAAATTGTTTTATGCAAAAATGCTTTTTAAACCAAACTAGTAACTGTAAAGAGAAGTTTTCAAAAATCA
+TTTTGCTCATATTTTTATAATTTTTTAAGAATGATTATGTCTGAAAAAAATTGTATGAAAAAAATACAGT
+GAAGGAGAGGTTTCCGACCCCATAAAGTATATATATTCGTGATCAGCGTCACTAGACGAGTCGACCTAGC
+CAAGTCCGTCTGTCCGTCCGTCTGTCTGTCTGTTTCTACGCAAACTAGTCTCTCATTTTTAAAGCTATCG
+GTCTGAAACTTTTCCAAAAGTCTTCTTTCTATTGCAGGTAGTATAAGTCGGAACCAGCCGGATTGAACAA
+CTATATTTTATAGCTCCCATATCGGGAAAAAAACTTTTAAAAAAATATATCCTTGGTGTTTTTTAGCATA
+TACCTTTCTATATATAACATTTTTATATTATATATATTATATATCATATAGCTCCCATAGGAACAATCGG
+AAATGGTAAAATAATATTTAAAAATTATATCTTCGGTGTTTTTTAACATATAACCTCCTAAGCTTAGAAT
+TAACATTTATTATTCGGTTTTGAATTTCGAATTAAATTTGATAAAAATAGGACGACTATATCATATAGCT
+GCCATAGTAACGACCGGAAAATTAGTCAGAAAACATGAAAATTATATCTTTGGTGTTTTTAACATATAAC
+TTTATAAGTTCGAAAATAACATTTTTTAATTAGTTCTGAATTTCGAATTAAATTTTATTAAAATCGGGCG
+ACTATATCATATAGCTGTCATAGGAACGATCGGTTAATTGGTGGGAAATAATATGAAACAAATTATAGAT
+TTTTATGCTTTTTGACATATTATCTTATTATATTGGGAATATAAATTTTTATATTTTTAAGAATTTCGAA
+TTAAATTTAATAAAATTATTGATTATTTTTTACAACTGCAAGGGCTTACCGAAGTTTGTATTCTTTCCTG
+TTTTTTATCGAAACCGGATAATTTTCTTGAAGCCCAATGTGGGTCGGTGTATTGAAAACTCAAAAACTTT
+CCGTCTTGCTTTGTGATCGAATTTTTTTCGAGTTTTTATGATACAATTTTACAATGTAGGCCATACACTG
+CTTCGACAAAATGGCTAAGCGTAACTAGAAATATATAGCACAAGTCTTAAAACAAGAAATTTAGTTAACT
+TCGGCAAGCCGAAGTTTGTATACCCTTGCAGTTATAAGAAATAATCAACGTTAGTAACACCATGTTAAAT
+TTTTAAGGATTATTGCTAGCTTTAGTGATGTTAAACAATGATTTCAATACTTCTTTGATACTTTTTTTAT
+AGCAATATTTTAGAGTGGTCCAATTTTTATTAATTTTAGTTTGAAATTCCTAAAAATATAAAGAATTATA
+TTCCCAATATTATAGAATTATATATCAAAAAACACCGAAGCTATAATTTGTTTTATATTATTTTTCCACC
+AATTTTCCGATCGTTCCTATGACAGCTATATGATATAGTCGTCCGATTTTAATAAAAATGTAATTCGAAA
+TTCACAACTAATTAAAAAATGTTATTTCCAAACGAAGAAGGTTATATGTTACAAAACACCAAAGATATAA
+TTTTTATACACGTTACTCGTAGAGTAAAAGGGTATACTAGTTTCGTCGGAAAGTATGTAACAAGTAGAAG
+GAAGGAAACGCTTCCCCTTAAAGTATATATATTTTTGATCAGGATCACTAGCCGAGTCGATCTAGCCATC
+ACCGTCTGTCTGTCTATCCGAATGAACGCTGAAATCTCGGAAACTATACAAGCAAACTTGGCAATCAAAT
+TCCTGGGCTTCCTGCGCAGCGCAAGTTTGTTTCAGCGGCATGCGACGCCCACTCTACACCCACAATTCGA
+GAAAATCTGTAGCGCCTACAGTATGATAGGATCAAAATTTAAAGTGAATTGTATTTGTCTCATCAATACC
+TATCGACTGACCAAAAAAACATGTGACATTTTTCACTCCCACTCTAACTTCCACAAACGGCTTAAACGGC
+TTGTTTTAAAATTGATTTCCGATAGTTCCTATGGGATCTATAAGATACAGTTGTCCGGTTCCGTCATATA
+TACTACATGCAATAGAAAAAAGACTTTTGTGAAAGTTTCAGCCCGATAGCTCTAAAACTGAGAGACTACA
+TTTCGTAGAAGCGGACGGACAGACGGACATGGCTTGTGACGCTGATCAAAAATATATATACGTCTCCTTC
+ACTGCGTTAGAAACTTCTGACTGAATTCATTATATAGATAGATATAGAACGCGAAAGGGCTCGTGCAGAC
Binary file test-data/KB462401.keepversion.2bit has changed
Binary file test-data/KB462401.masked.2bit has changed
Binary file test-data/KB462401.unmasked.2bit has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue May 16 14:50:20 2017 -0400
@@ -0,0 +1,57 @@
+<?xml version="1.0" ?>
+<tool_dependency>
+    <package name="ucsc_twobit" version="340">
+        <install version="1.0">
+            <actions_group>
+                <actions os="darwin" architecture="x86_64">
+                    <action type="download_by_url"
+                            sha256sum="aa0df6fc9c5dfe83cb94456e1100a5ecd7a247e7521d91f4e91c46c1b21fc9ab">
+                        http://old-gep.wustl.edu/~wilson/packages/ucsc_twobit/ucsc_twobit_340_macOS_x86_64.tar.gz
+                    </action>
+                    <action type="move_directory_files">
+                        <source_directory>bin</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+
+                <actions os="linux" architecture="x86_64">
+                    <action type="download_by_url"
+                            sha256sum="31b18fd6f0f24981815ded0a1790be49ca47a5d2cce40c3af29ffc6f5bea4922">
+                        http://old-gep.wustl.edu/~wilson/packages/ucsc_twobit/ucsc_twobit_340_linux_x86_64.tar.gz
+                    </action>
+                    <action type="move_directory_files">
+                        <source_directory>bin</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+
+                <!-- Display error message for unsupported OS and CPU architecture -->
+                <actions>
+                    <action type="shell_command">
+                        echo "ERROR: This package only supports 64-bit systems running macOS or Linux"
+                    </action>
+                    <action type="shell_command">false</action>
+                </actions>
+
+                <!-- update $PATH environment variable -->
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>
+        <![CDATA[
+            This package contains the utilities for constructing and manipulating
+            `twoBit files <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_.
+            The utilities were created by the
+            `Genome Bioinformatics Group <https://genome.ucsc.edu/staff.html>`_
+            at the UCSC Genomics Institute.
+
+            The twoBit file format is designed to store genomic sequences and the
+            associated repeat masking information. The twoBit file is used by the
+            UCSC Genome Browser and by tools such as
+            `BLAT <https://genome.ucsc.edu/goldenpath/help/blatSpec.html>`_.
+        ]]>
+        </readme>
+    </package>
+</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ucsc_macros.xml	Tue May 16 14:50:20 2017 -0400
@@ -0,0 +1,44 @@
+<macros>
+    <xml name="requirements_twobit">
+        <requirements>
+            <requirement type="package" version="340">ucsc_twobit</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <xml name="environment_LC_COLLATE">
+        <environment_variables>
+            <!-- Sort uppercase letters before lowercase (required by UCSC tools) -->
+            <environment_variable name="LC_COLLATE">C</environment_variable>
+            <yield />
+        </environment_variables>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+        @article{Kent01062002,
+author = {Kent, W. James and Sugnet, Charles W. and Furey, Terrence S. and Roskin, Krishna M. and Pringle, Tom H. and Zahler, Alan M. and Haussler,  and David},
+title = {The Human Genome Browser at UCSC},
+volume = {12},
+number = {6},
+pages = {996-1006},
+year = {2002},
+doi = {10.1101/gr.229102},
+URL = {http://genome.cshlp.org/content/12/6/996.abstract},
+eprint = {http://genome.cshlp.org/content/12/6/996.full.pdf+html},
+journal = {Genome Research}
+}
+            </citation>
+            <yield />
+        </citations>
+    </xml>
+
+    <token name="@OPTIONAL_PARAM_FUNC@">
+<![CDATA[
+        #def optional_param($_flag, $_flag_value, $_sep="=")
+            #if str($_flag_value) and str($_flag_value).strip():
+                ${_flag}${_sep}${_flag_value}
+            #end if
+        #end def
+]]>
+    </token>
+</macros>