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Changeset 3:877e80114d25 (2024-11-16)

Previous changeset 2:92b9fd5f1f9f (2024-01-27)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35

modified:
snipit.xml

diff -r 92b9fd5f1f9f -r 877e80114d25 snipit.xml
--- a/snipit.xml Sat Jan 27 23:29:55 2024 +0000
+++ b/snipit.xml Sat Nov 16 11:07:42 2024 +0000

[

b'@@ -1,7 +1,21 @@\n-<tool id="snipit" name="snipit" version="@TOOL_VERSION@+galaxy0">\n+<tool id="snipit" name="snipit" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">\n <description>Summarise snps relative to a reference sequence</description>\n <macros>\n- <token name="@TOOL_VERSION@">1.2</token>\n+ <token name="@TOOL_VERSION@">1.6</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <xml name="ref_select" token_help="">\n+ <conditional name="ref">\n+ <param name="select" type="select" label="The reference sequence ..."\n+ help="@HELP@">\n+ <option value="first">is the first sequence in the input</option>\n+ <option value="by_id">should be picked via its ID</option>\n+ </param>\n+ <when value="first" />\n+ <when value="by_id">\n+ <param name="id" argument="--reference" type="text" label="ID of reference sequence" />\n+ </when>\n+ </conditional>\n+ </xml>\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@@ -17,15 +31,41 @@\n <version_command>snipit -v</version_command>\n <command detect_errors="exit_code"><![CDATA[\n snipit \'$alignment\'\n- #if str($ref.select) == \'by_id\'\n+ --sequence-type $mode.sequence_type\n+ ## --cds-mode flag broken in this version of snipit\n+ ## but this is how it\'d be used.\n+ ##if str($mode.sequence_type) == \'nt\'\n+ ## $mode.cds_mode\n+ ##end if\n+ #if str($mode.ref.select) == \'by_id\'\n -r \'$ref.id\'\n #end if\n+ #if not str($mode.colouring.palette)\n+ --recombi-mode --recombi-references \'$mode.colouring.parent1,$mode.colouring.parent2\'\n+ #else\n+ -c $mode.colouring.palette\n+ #end if\n+ $pos_restrict.show_indels\n+ --ambig-mode $pos_restrict.ambig_mode\n+ #if len($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 #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+ $style.position_labels\n -f $plot.format\n #if str($plot.format) in [\'png\', \'svg\', \'tiff\']\n $plot.transparent_background\n@@ -39,20 +79,6 @@\n #end if\n $dims.size_option\n $style.flip_vertical\n- $show_indels\n- #if len($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- $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@@ -60,30 +86,66 @@\n #echo \',\'.join([str(p[\'p'..b'uring">\n <param name="palette" value="verity" />\n </conditional>\n- </section>\n+ </conditional>\n <conditional name="plot">\n <param name="format" value="jpg" />\n <param name="transparent_background" value="true" />\n@@ -239,6 +281,7 @@\n <test expect_num_outputs="1">\n <param name="alignment" value="input.fasta" />\n <section name="pos_restrict">\n+ <param name="ambig_mode" value="exclude" />\n <repeat name="include_positions">\n <param name="pos" value="1-10000" />\n </repeat>\n@@ -248,7 +291,6 @@\n <repeat name="exclude_positions">\n <param name="pos" value="1000-2000" />\n </repeat>\n- <param name="exclude_ambig_pos" value="true" />\n </section>\n <section name="style">\n <conditional name="sort">\n@@ -272,7 +314,7 @@\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="--ambig-mode exclude" />\n <has_text text="--sort-by-mutations 3,1,2" />\n <has_text text="--high-to-low" />\n </assert_command>\n@@ -281,7 +323,7 @@\n \n- <not_has_text text="" />\n+ <has_line_matching expression=".*<text .+>1059</text>" negate="true" />\n <has_text text="style="fill: #8fbc8f" />\n <not_has_text text="style="fill: #ffffff"" />\n </assert_contents>\n@@ -289,17 +331,17 @@\n </test>\n <test expect_num_outputs="1">\n <param name="alignment" value="input.fasta" />\n- <conditional name="ref">\n- <param name="select" value="by_id" />\n- <param name="id" value="reference" />\n- </conditional>\n- <section name="style">\n+ <conditional name="mode">\n+ <conditional name="ref">\n+ <param name="select" value="by_id" />\n+ <param name="id" value="reference" />\n+ </conditional>\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>\n <conditional name="plot">\n <param name="format" value="svg" />\n </conditional>\n@@ -309,7 +351,7 @@\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="" />\n+ <has_line_matching expression=".*<text .+>1059</text>" />\n <has_text text="style="fill: #daa520" />\n <has_text text="style="fill: #ea5463" />\n <has_text text="style="fill: #ffffff"" />\n@@ -343,7 +385,7 @@\n <help><![CDATA[\n **What it does**\n \n-Snipit finds the SNPs relative to a reference in a multiple sequence alignment and highlights these changes as a figure.\n+Snipit finds mutations relative to a reference in a multiple sequence alignment and presents these changes in a nice overview plot.\n ]]>\n </help>\n <citations>\n'