| Next changeset 1:260f7da5a7e5 (2016-03-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot commit e709cda2e1a3526a66e5af067772a1c5bee205be |
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added:
FourColorPlot.jar fasta_nucleotide_color_plot.xml macros.xml test-data/input.fasta test-data/output1.png test-data/output2.png |
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| diff -r 000000000000 -r 980917b09eb8 FourColorPlot.jar |
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| Binary file FourColorPlot.jar has changed |
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| diff -r 000000000000 -r 980917b09eb8 fasta_nucleotide_color_plot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fasta_nucleotide_color_plot.xml Sun Mar 06 13:45:42 2016 -0500 |
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| @@ -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> |
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| diff -r 000000000000 -r 980917b09eb8 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Mar 06 13:45:42 2016 -0500 |
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| @@ -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> |
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| diff -r 000000000000 -r 980917b09eb8 test-data/input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fasta Sun Mar 06 13:45:42 2016 -0500 |
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| @@ -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 |
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