Mercurial > repos > iuc > fasta_nucleotide_color_plot

changeset 0:980917b09eb8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot commit e709cda2e1a3526a66e5af067772a1c5bee205be
author iuc
date Sun, 06 Mar 2016 13:45:42 -0500
parents
children 260f7da5a7e5
files FourColorPlot.jar fasta_nucleotide_color_plot.xml macros.xml test-data/input.fasta test-data/output1.png test-data/output2.png
diffstat 6 files changed, 265 insertions(+), 0 deletions(-) [+]
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Binary file FourColorPlot.jar has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_nucleotide_color_plot.xml	Sun Mar 06 13:45:42 2016 -0500
@@ -0,0 +1,153 @@
+<tool id="four_color_plot" name="Fasta nucleotide color plot" version="1.0.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+        <![CDATA[
+            java -jar $__tool_directory__/FourColorPlot.jar
+            -f "$input"
+            -h $pixel_height
+            -w $pixel_width
+            #if str($a_select_color_cond.a_select_color) == "a_rgb":
+                -A "$a_select_color_cond.a_rgb"
+            #else:
+                -A $a_select_color_cond.color_a
+            #end if
+            #if str($t_select_color_cond.t_select_color) == "t_rgb":
+                -T "$t_select_color_cond.t_rgb"
+            #else
+                -T $t_select_color_cond.color_t
+            #end if
+            #if str($g_select_color_cond.g_select_color) == "g_rgb":
+                -G "$g_select_color_cond.g_rgb"
+            #else
+                -G $g_select_color_cond.color_g
+            #end if
+            #if str($c_select_color_cond.c_select_color) == "c_rgb":
+                -C "$c_select_color_cond.c_rgb"
+            #else
+                -C $c_select_color_cond.color_c
+            #end if
+            #if str($n_select_color_cond.n_select_color) == "n_rgb":
+                -N "$n_select_color_cond.n_rgb"
+            #else
+                -N $n_select_color_cond.color_n
+            #end if
+            -o "$output" 1>/dev/null
+        ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="FASTA file" />
+        <param name="pixel_height" type="integer" value="2" min="1" label="Pixel height per nucleotide" />
+        <param name="pixel_width" type="integer" value="2" min="1" label="Pixel width per nucleotide" />
+        <conditional name="a_select_color_cond">
+            <param name="a_select_color" type="select" label="A nucleotide: specify RGB value or select color?">
+                <option value="a_rgb" selected="True">specify RGB</option>
+                <option value="a_color">select color</option>
+            </param>
+            <when value="a_color">
+                <param name="color_a" type="select" label="Color">
+                    <expand macro="color_selector" />
+                </param>
+            </when>
+            <when value="a_rgb">
+                <param name="a_rgb" type="text" value="254,25,24" label="RGB" />
+            </when>
+        </conditional>
+        <conditional name="t_select_color_cond">
+            <param name="t_select_color" type="select" label="T nucleotide: specify RGB value or select color?">
+                <option value="t_rgb" selected="True">specify RGB</option>
+                <option value="t_color">select color</option>
+            </param>
+            <when value="t_color">
+                <param  name="color_t" type="select" label="Color">
+                    <expand macro="color_selector" />
+                </param>
+            </when>
+            <when value="t_rgb">
+                <param name="t_rgb" type="text" value="50,204,60" label="RGB" />
+            </when>
+        </conditional>
+        <conditional name="g_select_color_cond">
+            <param name="g_select_color" type="select" label="G nucleotide: specify RGB value or select color?">
+                <option value="g_rgb" selected="True">specify RGB</option>
+                <option value="g_color">select color</option>
+            </param>
+            <when value="g_color">
+                <param  name="color_g" type="select" label="Color">
+                    <expand macro="color_selector" />
+                </param>
+            </when>
+            <when value="g_rgb">
+                <param name="g_rgb" type="text" value="252,252,80" label="RGB" />
+            </when>
+        </conditional>
+        <conditional name="c_select_color_cond">
+            <param name="c_select_color" type="select" label="C nucleotide: specify RGB value or select color?">
+                <option value="c_rgb" selected="True">specify RGB</option>
+                <option value="c_color">select color</option>
+            </param>
+            <when value="c_color">
+                <param  name="color_c" type="select" label="Color">
+                    <expand macro="color_selector" />
+                </param>
+            </when>
+            <when value="c_rgb">
+                <param name="c_rgb" type="text" value="43,49,246" label="RGB" />
+            </when>
+        </conditional>
+        <conditional name="n_select_color_cond">
+            <param name="n_select_color" type="select" label="N nucleotide: specify RGB value or select color?">
+                <option value="n_rgb" selected="True">specify RGB</option>
+                <option value="n_color">select color</option>
+            </param>
+            <when value="n_color">
+                <param  name="color_n" type="select" label="Color">
+                    <expand macro="color_selector" />
+                </param>
+            </when>
+            <when value="n_rgb">
+                <param name="n_rgb" type="text" value="128,128,128" label="RGB" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output" format="png" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="input.fasta" ftype="fasta" />
+            <output name="output" file="output1.png" ftype="png" compare="sim_size" />
+        </test>
+        <test>
+            <param name="input" value="input.fasta" ftype="fasta" />
+            <param name="color_a" value="255,0,0" />
+            <param name="color_t" value="0,255,0" />
+            <param name="color_g" value="0,0,255" />
+            <param name="color_c" value="255,255,0" />
+            <param name="color_n" value="128,0,128" />
+            <output name="output" file="output2.png" ftype="png" compare="sim_size" />
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+Produces a graphical representation of FASTA data with each nucleotide represented by a selected color.
+
+-----
+
+**Options**
+
+* **Pixel Height per Nucleotide** - height of each nucleotide in pixels
+* **Pixel Width per Nucleotide** - width of each nucleotide in pixels
+* **A Color** - color of A nucleotide
+* **T Color** - color of T nucleotide
+* **G Color** - color of G nucleotide
+* **C Color** - color of C nucleotide
+* **N Color** - color of N nucleotide
+
+    </help>
+    <expand macro="citations" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sun Mar 06 13:45:42 2016 -0500
@@ -0,0 +1,24 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<macros>
+    <xml name="color_selector">
+        <option value="255,0,0" selected="True">red</option>
+        <option value="0,255,0">green</option>
+        <option value="0,0,255">blue</option>
+        <option value="255,255,0">yellow</option>
+        <option value="128,0,128">purple</option>
+        <option value="255,165,0">orange</option>
+        <option value="0,0,0">black</option>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @unpublished{None,
+                author = {Lai, William},
+                title = {None},
+                year = {None},
+                eprint = {None},
+                url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
+            }</citation>
+        </citations>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.fasta	Sun Mar 06 13:45:42 2016 -0500
@@ -0,0 +1,88 @@
+>hg17_chr1_147962192_147962580_-
+ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTG
+GACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGT
+GATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGT
+CCCTGTTCGTGAGGTCTGTCCAGTGACCCATCGTCCAGCCCTATACCGGG
+ACCCTGTTACAGACATACCCTATGCCACTGCTCGAGCCTTCAAGATCATT
+CGTGAGGCTTACAAGAAGTACATTACTGCCCATGGACTGCCGCCCACTGC
+CTCAGCCCTGGGCCCCGGCCCGCCACCTCCTGAGCCCCTCCCTGGCTCTG
+GGCCCCGAGCCTTGCGCCAGAAAATTGTCATTAAATGA
+>hg17_chr1_147984545_147984630_+
+ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTT
+TGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+>hg17_chr1_148078400_148078582_-
+GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAA
+GAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGA
+GCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACG
+GCTTCCAGTACCTCACCAACGGCATCATGTGA
+>hg17_chr1_148185136_148185276_+
+ATGGAAGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGGGTCCGGC
+CCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATC
+CGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA
+>hg17_chr10_55251623_55253124_-
+TCTTTTCCTTCTCTACCATTTTCAACAAAGCAGGGGAAATAACTCAGTCT
+CAGAAGACAGGAAACATCAACAAGTTGTGATGCCCTTTTCTTCCAATACT
+ATTGAGGCTCACAAGTCAGCTCATGTAGACGGATCACTTAAGAGCAACAA
+ACTGAAGTCTGCAAGAAAATTCACATTTCTATCTGATGAGGATGACTTAA
+GTGCCCATAATCCCCTTTATAAGGAAAACATAAGTCAAGTATCAACAAAT
+TCAGACATTTCACAGAGAACAGATTTTGTAGACCCATTTTCACCCAAAAT
+ACAAGCCAAGAGTAAGTCTCTGAGGGGCCCAAGAGAAAAGATTCAGAGGC
+TGTGGAGTCAGTCAGTCAGCTTACCCAGGAGGCTGATGAGGAAAGTTCCA
+AATAGACCAGAGATCATAGATCTGCAGCAGTGGCAAGGCACCAGGCAGAA
+AGCTGAAAATGAAAACACTGGAATCTGTACAAACAAAAGAGGTAGCAGCA
+ATCCATTGCTTACAACTGAAGAGGCAAATTTGACAGAGAAAGAGGAAATA
+AGGCAAGGTGAAACACTGATGATAGAAGGAACAGAACAGTTGAAATCTCT
+CTCTTCAGACTCTTCATTTTGCTTTCCCAGGCCTCACTTCTCATTCTCCA
+CTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATCAGAACCTAATGTC
+ATCAGTTCTCCTGCTGAGTGTTCCTTGGAACTTTCTCCTTCAAGGCCTTG
+TGTTTTACATTCTTCACTCTCTAGGAGAGAGACACCTATTTGTATGTTAC
+CTATTGAAACCGAAAGAAATATTTTTGAAAATTTTGCCCATCCACCAAAC
+ATCTCTCCTTCTGCCTGtccccttccccctcctcctcctatttctcctcc
+ttctcctcctcctgctcctgctcctcttgctcctcctcctgacatttctc
+ctttttctcttttttgtcctcctccctctcctccttctatccctcttcct
+cttcctcctcctACATTTTTTCCACTTTCCGTTTCAACGTCTGGTCCCCC
+AACAccacctcttctacctccatttccaactcctcttcctccaccacctc
+cttctattccttgccctccacctccttcAGCTTCATTTCTGTCCACAGAG
+TGTGTCTGTATAACAGGTGTTAAATGCACGACCAACTTGATGCCTGCCGA
+GAAAATTAAGTCCTCTATGACACAGCTATCAACAACGACAGTGTGTAAAA
+CAGACCCTCAGAGAGAACCAAAAGGCATCCTCAGACACGTTAAAAACTTA
+GCAGAACTTGAAAAATCAGTAGCTAACATGTACAGTCAAATAGAAAAAAA
+CTATCTACGCACAAATGTTTCAGAACTTCAAACTATGTGCCCTTCAGAAG
+TAACAAATATGGAAATCACATCTGAACAAAACAAGGGGAGTTTGAACAAT
+ATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAATCTACTTCACTGTA
+A
+>hg17_chr11_116124407_116124501_-
+ATCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGG
+CAGTGGAGGAACTTGCCTACAAATGGAGTGTTGAGGATATGTAA
+>hg17_chr11_116206508_116206563_+
+ATGCAGCCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTGGCCTC
+TGCCC
+>hg17_chr11_116211733_116212337_-
+CCTAAAGCTCCTTGACAACTGGGACAGCGTGACCTCCACCTTCAGCAAGC
+TGCGCGAACAGCTCGGCCCTGTGACCCAGGAGTTCTGGGATAACCTGGAA
+AAGGAGACAGAGGGCCTGAGGCAGGAGATGAGCAAGGATCTGGAGGAGGT
+GAAGGCCAAGGTGCAGCCCTACCTGGACGACTTCCAGAAGAAGTGGCAGG
+AGGAGATGGAGCTCTACCGCCAGAAGGTGGAGCCGCTGCGCGCAGAGCTC
+CAAGAGGGCGCGCGCCAGAAGCTGCACGAGCTGCAAGAGAAGCTGAGCCC
+ACTGGGCGAGGAGATGCGCGACCGCGCGCGCGCCCATGTGGACGCGCTGC
+GCACGCATCTGGCCCCCTACAGCGACGAGCTGCGCCAGCGCTTGGCCGCG
+CGCCTTGAGGCTCTCAAGGAGAACGGCGGCGCCAGACTGGCCGAGTACCA
+CGCCAAGGCCACCGAGCATCTGAGCACGCTCAGCGAGAAGGCCAAGCCCG
+CGCTCGAGGACCTCCGCCAAGGCCTGCTGCCCGTGCTGGAGAGCTTCAAG
+GTCAGCTTCCTGAGCGCTCTCGAGGAGTACACTAAGAAGCTCAACACCCA
+GTGA
+>hg17_chr11_1812377_1812407_+
+ATGCTCCACCTGCATGGCTGGCAAACCATG
+>hg17_chr12_38440094_38440321_-
+GAGCTTTCTTCCTCTATGCTGGATTTGCTGCTGTGGGACTCCTTTTCATC
+TATGGCTGTCTTCCTGAGACCAAAGGCAAAAAATTAGAGGAAATTGAATC
+ACTCTTTGACAACAGGCTATGTACATGTGGCACTTCAGATTCTGATGAAG
+GGAGATATATTGAATATATTCGGGTAAAGGGAAGTAACTATCATCTTTCT
+GACAATGATGCTTCTGATGTGGAATAA
+>hg17_chr13_112381694_112381953_+
+ATGAACTCACCAGAGGCGAGGCTCTGCGTTGCTCAATGCAGAGACTCTTA
+CCCAGGGTGTCAGCCTCTGAAAGATACACGTGCCTGGGCCTCTTCCCTGA
+AGATGGACCCGGCAGGTCTGGAGGGAGGCCCCCGTGATGAATCCCGTGAT
+GAGCCGCCGATCCGAGCTCAGGCTGCGTCATGGGACCAGCCACAAGGTTG
+CCTGACCTATAAAGGTCGCAGGAGTGCCTCAGGGACACAGAAGCAGTTAC
+AGCTGCCAG
Binary file test-data/output1.png has changed
Binary file test-data/output2.png has changed