| Previous changeset 6:690c2caa367e (2022-12-05) Next changeset 8:6ec1b853c8fd (2024-10-10) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a |
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modified:
gfastats.xml macros.xml test-data/swiss_army.sak test-data/test_01.fasta.gz |
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| diff -r 690c2caa367e -r 3ef480892a9f gfastats.xml --- a/gfastats.xml Mon Dec 05 12:20:31 2022 +0000 +++ b/gfastats.xml Fri Dec 23 20:00:51 2022 +0000 |
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| b'@@ -35,13 +35,14 @@\n #end if\n $mode_condition.discover_paths\n -o dataset.$mode_condition.output_condition.out_format\n- #if $mode_condition.output_condition.out_format == \'fasta\'\n+ #if $mode_condition.output_condition.out_format in [\'fasta\',\'fasta.gz\']\n #if $mode_condition.output_condition.line_length\n --line-length $mode_condition.output_condition.line_length\n #end if\n- #else if $mode_condition.output_condition.out_format == \'fasta.gz\'\n- #if $mode_condition.output_condition.line_length\n- --line-length $mode_condition.output_condition.line_length\n+ #end if\n+ #if $mode_condition.output_condition.out_format in [\'gfa\',\'gfa.gz\']\n+ #if $mode_condition.output_condition.terminal_overlaps_condition.terminal_overlaps_select == \'yes\':\n+ --discover-terminal-overlaps $mode_condition.output_condition.terminal_overlaps_condition.terminal_overlaps_length\n #end if\n #end if\n #else if $mode_condition.selector == "statistics"\n@@ -55,6 +56,7 @@\n --seq-report\n $mode_condition.statistics_condition.out_sequence\n #end if\n+ $mode_condition.locale\n $mode_condition.discover_paths\n $mode_condition.tabular > \'$stats\'\n #else\n@@ -93,10 +95,10 @@\n <param argument="--include-bed" type="data" optional="true"\n format="bed" label="Include specific intervals"\n help="Generates output on a subset list of headers or coordinates \n- in 0-based bed format. It can be combined with --exclude-bed. Optional"/>\n+ in 0-based bed format. It can be combined with --exclude-bed. Optional."/>\n <param argument="--exclude-bed" type="data" format="bed" optional="true"\n label="Exclude specific intervals"\n- help="Exclude a subset of headers or coordinates in 0-base bed format. It can be conmbined with --include-bed Optional"/>\n+ help="Exclude a subset of headers or coordinates in 0-base bed format. It can be conmbined with --include-bed. Optional."/>\n </when>\n <when value="false"/>\n </conditional>\n@@ -128,19 +130,23 @@\n </when>\n <when value="fastq"/>\n <when value="fastq.gz"/>\n- <when value="gfa"/>\n- <when value="gfa.gz"/>\n-\t\t</conditional>\n- <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly \n- is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" />\n- <param argument="--sort" type="select" label="Sort sequences" help="Specify how to sort the sequences. Ascending/descending used the sequence/path header.">\n+ <when value="gfa">\n+ <expand macro="terminal_overlaps_macro"/>\n+ </when>\n+ <when value="gfa.gz">\n+ <expand macro="terminal_overlaps_macro"/>\n+ </when>\n+\t\t </conditional>\n+ <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space, an assembly \n+ is a collection of segments and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence." />\n+ '..b' </conditional>\n+ <param argument="--locale" type="boolean" truevalue="--locale en_US.UTF-8" falsevalue="" checked="true"\n+ label="Thousands separator in output" help="Use commas for thousands separator in output?"/>\n <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true"\n label="Tabular-format output" help="Generate output in tabular format"/>\n <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly \n@@ -211,10 +219,6 @@\n <!--Test 01 -->\n <test expect_num_outputs="1">\n <param name="input_file" value="dataset_01.fastq.gz"/>\n- <conditional name="target_condition">\n- <param name="target_condition" value="true"/>\n- <param name="target_sequence" value="S1_1"/>\n- </conditional>\n <conditional name="mode_condition">\n <param name="selector" value="manipulation"/>\n <param name="swiss_army_knife" value="swiss_army.sak"/>\n@@ -237,10 +241,11 @@\n <param name="selector" value="size"/>\n <param name="out_size" value="c"/>\n </conditional>\n+ <param name="locale" value="false"/>\n </conditional>\n <output name="stats" ftype="tabular">\n <assert_contents>\n- <has_text text="S1_76.1	9445" />\n+ <has_text text="S1_1.1	8550" />\n </assert_contents>\n </output>\n </test>\n@@ -252,6 +257,7 @@\n <conditional name="statistics_condition">\n <param name="selector" value="sequence"/>\n </conditional>\n+ <param name="locale" value="false"/>\n </conditional>\n <output name="stats" ftype="tabular">\n <assert_contents>\n@@ -268,6 +274,7 @@\n <param name="selector" value="assembly"/>\n <param name="expected_genomesize" value="600000"/>\n </conditional>\n+ <param name="locale" value="false"/>\n </conditional>\n <output name="stats" value="test_04_stats.tabular" ftype="tabular"/>\n </test>\n@@ -280,6 +287,7 @@\n <param name="selector" value="coordinates"/>\n <param name="out_coord" value="a"/>\n </conditional>\n+ <param name="locale" value="false"/>\n </conditional>\n <output name="stats" value="test_05_stats.tabular" ftype="tabular"/>\n </test>\n@@ -302,6 +310,7 @@\n <conditional name="statistics_condition">\n <param name="selector" value="assembly"/>\n </conditional>\n+ <param name="locale" value="false"/>\n <param name="tabular" value="false"/>\n </conditional>\n <output name="stats" value="test_07_stats.tabular" ftype="tabular"/>\n@@ -347,6 +356,9 @@\n <param name="target_option" value="true"/>\n <param name="include_bed" value="regions.bed"/>\n </conditional>\n+ <conditional name="mode_condition">\n+ <param name="locale" value="false"/>\n+ </conditional>\n <output name="stats" value="test_11_stats.tabular" ftype="tabular"/>\n </test>\n <!--Test 12 -->\n@@ -357,6 +369,7 @@\n <conditional name="statistics_condition">\n <param name="selector" value="assembly"/>\n </conditional>\n+ <param name="locale" value="false"/>\n <param name="tabular" value="false"/>\n <param name="discover_paths" value="true"/>\n </conditional>\n' |
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| diff -r 690c2caa367e -r 3ef480892a9f macros.xml --- a/macros.xml Mon Dec 05 12:20:31 2022 +0000 +++ b/macros.xml Fri Dec 23 20:00:51 2022 +0000 |
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| @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">1.3.5</token> - <token name="@SUFFIX_VERSION@">2</token> + <token name="@TOOL_VERSION@">1.3.6</token> + <token name="@SUFFIX_VERSION@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">gfastats</requirement> @@ -26,7 +26,22 @@ </xml> <xml name="length_macro"> <param argument="--line-length" type="integer" min="0" max="80" value="" - optional="true" label="Especify line length" - help="Specifies line length when output format is fasta. Default has no line breaks."/> + optional="true" label="Specify line length" + help="Optional: specifies line length when output format is fasta. Default has no line breaks."/> + </xml> + <xml name="terminal_overlaps_macro"> + <conditional name="terminal_overlaps_condition"> + <param name="terminal_overlaps_select" type="select" + label="Terminal overlaps selection" help="Optional: Do you want to detect terminal overlaps?"> + <option value="no">No (default)</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="terminal_overlaps_length" type="integer" min="500" value="500" + optional="false" label="Terminal overlaps length" + help="Integer for minimum length required to count as an overlap for detecting terminal overlaps (minimum is 500)" /> + </when> + </conditional> </xml> </macros> |
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| diff -r 690c2caa367e -r 3ef480892a9f test-data/swiss_army.sak --- a/test-data/swiss_army.sak Mon Dec 05 12:20:31 2022 +0000 +++ b/test-data/swiss_army.sak Fri Dec 23 20:00:51 2022 +0000 |
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| @@ -1,1 +1,1 @@ -REMOVE s1_1 +REMOVE S1_1.1 |
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| diff -r 690c2caa367e -r 3ef480892a9f test-data/test_01.fasta.gz |
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| Binary file test-data/test_01.fasta.gz has changed |