| Previous changeset 0:20b4c59bec12 (2022-07-17) Next changeset 2:92b9fd5f1f9f (2024-01-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d |
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modified:
snipit.xml |
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added:
test-data/custom_labels.csv test-data/snps.csv |
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| diff -r 20b4c59bec12 -r 9f23fe0cb70b snipit.xml --- a/snipit.xml Sun Jul 17 15:01:31 2022 +0000 +++ b/snipit.xml Fri Oct 28 20:58:45 2022 +0000 |
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| b'@@ -1,108 +1,330 @@\n <tool id="snipit" name="snipit" version="@TOOL_VERSION@+galaxy0">\n <description>Summarise snps relative to a reference sequence</description>\n <macros>\n- <token name="@TOOL_VERSION@">1.0.5</token>\n+ <token name="@TOOL_VERSION@">1.0.7</token>\n+ <xml name="handle_background" tokens="format">\n+ <when value="@FORMAT@">\n+ <param argument="--solid-background" name="transparent_background" type="boolean" truevalue="" falsevalue="--solid-background" label="Plot on transparent background?" />\n+ </when>\n+ </xml>\n </macros>\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">snipit</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n- snipit \'$alignment\'\n- #if $opt.reference\n- -r \'$opt.reference\'\n+ MPLCONFIGDIR=.matplotlib snipit \'$alignment\'\n+ #if str($ref.select) == \'by_id\'\n+ -r \'$ref.id\'\n+ #end if\n+ #if str($style.labels.choose)\n+ -l \'$style.labels.source\'\n+ #if str($style.labels.choose) == \'custom_csv\'\n+ --l-header \'${style.labels.names_column},${style.labels.labels_column}\'\n+ #end if\n #end if\n- #if $opt.labels\n- -l \'$opt.labels\'\n+ -f $plot.format\n+ #if str($plot.format) in [\'png\', \'svg\', \'tiff\']\n+ $plot.transparent_background\n+ #end if\n+ $write_snps\n+ #if $dims.height > 0\n+ --height $dims.height\n+ #end if\n+ #if $dims.width > 0\n+ --width $dims.width\n #end if\n- --l-header \'$opt.l_header\'\n- -f \'$opt.format\'\n- --height \'$opt.height\'\n- --width \'$opt.width\'\n- --size-option \'$opt.size_option\'\n- $opt.flip_vertical\n- #if $opt.exclude_positions\n- --exclude-positions \'$opt.exclude_positions\'\n+ $dims.size_option\n+ $style.flip_vertical\n+ #if len($pos_restrict.include_positions)\n+ --include-positions\n+ #for $p in $pos_restrict.include_positions\n+ \'$p.pos\'\n+ #end for\n+ #end if\n+ #if len($pos_restrict.exclude_positions)\n+ --exclude-positions\n+ #for $p in $pos_restrict.exclude_positions\n+ \'$p.pos\'\n+ #end for\n #end if\n- $opt.exclude_ambig_pos\n- $opt.sort_by_mutation_number\n- $opt.sort_by_id\n- #if $opt.sort_by_mutations\n- --sort-by-mutations \'$opt.sort_by_mutations\'\n+ $pos_restrict.exclude_ambig_pos\n+ $style.sort.order\n+ #if str($style.sort.order) == \'--sort-by-mutation-number\'\n+ $style.sort.high_to_low\n+ #else if str($style.sort.order) == \'--sort-by-mutations\'\n+ #echo \',\'.join([str(p[\'pos\']) for p in $style.sort.positions])\n+ $style.sort.high_to_low\n #end if\n- $opt.high_to_low\n- -c \'$opt.colour_palette\'\n- ]]> </command>\n+ #if not str($style.colouring.palette)\n+ --recombi-mode --recombi-references \'$style.colouring.parent1,$style.colouring.parent2\'\n+ #else\n+ -c $style.colouring.palette\n+ #end if\n+ ]]></command>\n <inputs>\n <param name="alignment" format="fasta" type="data" label="Input alignment fasta file" />\n- <section name="opt" title="Optional arguments" expanded="true">\n- <param name="reference" argument="-r" type="text" optional="true" label="Reference sequence (by sequence ID)" help="Indicates which sequence in the alignment is the reference (by sequence ID). Default: first sequence in alignment" />\n- '..b'ons" />\n+ <repeat name="positions">\n+ <param name="pos" value="3" />\n+ </repeat>\n+ <repeat name="positions">\n+ <param name="pos" value="1" />\n+ </repeat>\n+ <repeat name="positions">\n+ <param name="pos" value="2" />\n+ </repeat>\n+ <param name="high_to_low" value="true" />\n+ </conditional>\n+ </section>\n+ <conditional name="plot">\n+ <param name="format" value="svg" />\n+ <param name="transparent_background" value="true" />\n+ </conditional>\n+ <assert_command>\n+ <has_text text="--include-positions \'1-10000\' \'10001-30000\'" />\n+ <has_text text="--exclude-positions \'1000-2000\'" />\n+ <has_text text="--exclude-ambig-pos" />\n+ <has_text text="--sort-by-mutations 3,1,2" />\n+ <has_text text="--high-to-low" />\n+ </assert_command>\n+ <output name="snp_plot" ftype="svg">\n+ <assert_contents>\n+ <!-- check that the plot does NOT refer to excluded\n+ position 1059, uses darkseagreen (to highlight Ts) and\n+ transparent (i.e. NOT white) background -->\n+ <not_has_text text="<!-- 1059 -->" />\n+ <has_text text="style="fill: #8fbc8f" />\n+ <not_has_text text="style="fill: #ffffff"" />\n+ </assert_contents>\n+ </output>\n </test>\n+ <test expect_num_outputs="1">\n+ <param name="alignment" value="input.fasta" />\n+ <section name="style">\n+ <conditional name="colouring">\n+ <param name="palette" value="" />\n+ <param name="parent1" value="USA_1" />\n+ <param name="parent2" value="USA_5" />\n+ </conditional>\n+ </section>\n+ <conditional name="plot">\n+ <param name="format" value="svg" />\n+ </conditional>\n+ <output name="snp_plot" ftype="svg">\n+ <assert_contents>\n+ <!-- check that the plot does mention position 1059,\n+ uses goldenrod and #EA5463 as colors (to\n+ indicate private and parent2 mutations, respectively, in\n+ recombi-mode) and uses a solid white background -->\n+ <has_text text="<!-- 1059 -->" />\n+ <has_text text="style="fill: #daa520" />\n+ <has_text text="style="fill: #ea5463" />\n+ <has_text text="style="fill: #ffffff"" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="alignment" value="input.fasta" />\n+ <section name="style">\n+ <conditional name="labels">\n+ <param name="choose" value="custom_csv" />\n+ <param name="source" value="custom_labels.csv" />\n+ <param name="names_column" value="ori" />\n+ <param name="labels_column" value="new" />\n+ </conditional>\n+ </section>\n+ <conditional name="plot">\n+ <param name="format" value="svg" />\n+ </conditional>\n+ <output name="snp_plot" ftype="svg">\n+ <assert_contents>\n+ <!-- check that the plot does not mention the original\n+ seq IDs but the mapped labels -->\n+ <not_has_text text="USA_" />\n+ <has_text text="SAMPLE_" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+\n </tests>\n <help><![CDATA[\n **What it does**\n' |
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| diff -r 20b4c59bec12 -r 9f23fe0cb70b test-data/custom_labels.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/custom_labels.csv Fri Oct 28 20:58:45 2022 +0000 |
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| @@ -0,0 +1,7 @@ +ori,new +USA_1,SAMPLE_1 +USA_2,SAMPLE_2 +USA_3,SAMPLE_3 +USA_4,SAMPLE_4 +USA_5,SAMPLE_5 +reference,reference |
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| diff -r 20b4c59bec12 -r 9f23fe0cb70b test-data/snps.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snps.csv Fri Oct 28 20:58:45 2022 +0000 |
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| @@ -0,0 +1,6 @@ +record,snps,num_snps +USA_1,1059CT;3037CT;8782TC;14408CT;23403AG;25563GT;28144CT,52 +USA_2,15240CT;17747CT;17858AG;18060CT;21774CT,39 +USA_3,1059CT;3037CT;8782TC;13006TC;14408CT;23403AG;25563GT;25688CT;28144CT,68 +USA_4,2005CA;2749CA;3037CT;8782TC;14408CT;20268AG;23403AG;28144CT,59 +USA_5,17747CT;17858AG;18060CT;20281TC,31 |