diff --git a/tools/minimap2/macros.xml b/tools/minimap2/macros.xml index 6234293c0a0..aadd8937233 100644 --- a/tools/minimap2/macros.xml +++ b/tools/minimap2/macros.xml @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.28</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="edam_ontology"> <edam_topics> <edam_topic>topic_0102</edam_topic> diff --git a/tools/minimap2/minimap2.xml b/tools/minimap2/minimap2.xml index 8435713747e..b8a2f01b411 100644 --- a/tools/minimap2/minimap2.xml +++ b/tools/minimap2/minimap2.xml @@ -141,6 +141,9 @@ #if $io_options.K: -K $io_options.K #end if + #if $io_options.eqx: + --eqx + #end if -t \${GALAXY_SLOTS:-4} reference.fa #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']: @@ -164,7 +167,6 @@ -T "\${TMPDIR:-.}" -@\${GALAXY_SLOTS:-2} -O $io_options.output_format - $io_options.eqx --reference reference.fa --output-fmt-option no_ref -o '$alignment_output' diff --git a/tools/mummer4/macros.xml b/tools/mummer4/macros.xml index 1492edc3201..84f67fa9ea9 100644 --- a/tools/mummer4/macros.xml +++ b/tools/mummer4/macros.xml @@ -11,7 +11,7 @@ </citations> </xml> <token name="@TOOL_VERSION@">4.0.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">20.05</token> <xml name="gnuplot_requirement"> <requirement type="package" version="5.4.10">gnuplot</requirement> diff --git a/tools/mummer4/show-coords.xml b/tools/mummer4/show-coords.xml index 6f51d996c66..7dcb144a93f 100755 --- a/tools/mummer4/show-coords.xml +++ b/tools/mummer4/show-coords.xml @@ -9,6 +9,7 @@ <![CDATA[ show-coords $merge + $direction -c -H -I '$identity' @@ -17,7 +18,12 @@ $annotate $sort -T - '${delta}' > '${output}' + '${delta}' + #if $direction: + > '${output_extend}' + #else: + > '${output}' + #end if ]]> </command> <inputs> @@ -25,6 +31,8 @@ <param name="merge" type="boolean" argument="-b" truevalue="-b" falsevalue="" label="Merge" help="Merges overlapping alignments regardless of match dir or frame and does not display any idenitity information. (-b)" /> <param name="identity" type="float" argument="-I" value="75.0" label="Identity" help="Set minimum percent identity to display (-I)" /> + + <param name="direction" type="boolean" argument="-d" truevalue="-d" falsevalue="" label="Direction" help="Display the alignment direction in the additional FRM columns (-d)" /> <param name="min_alignment_length" type="integer" argument="-L" value="100" label="Minimum Alignment Length" help="Set minimum alignment length to display (-L)" /> <param name="annotate" type="boolean" argument="-o" truevalue="-o" falsevalue="" label="Annotate" help="Annotate maximal alignments between two sequences, i.e. overlaps between reference and query sequences (-o)" /> @@ -32,24 +40,38 @@ <option value="-q">Sort output by query IDs and coordinates (-q)</option> <option value="-r">Sort output by reference IDs and coordinates (-r)</option> </param> + </inputs> <outputs> - <data name="output" format="tabular" from_work_dir="show-coords.txt" > + <data name="output" format="tabular" from_work_dir="show-coords.txt" label="${tool.name} on ${on_string} default format)"> + <filter>direction is False</filter> <actions> <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [REF TAG], [QUERY TAG]" /> </actions> </data> + <data name="output_extend" format="tabular" from_work_dir="show-coords_extend.txt" label="${tool.name} on ${on_string} extend format)" > + <filter>direction is True</filter> + <actions> + <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [FRM R], [FRM Q], [REF TAG], [QUERY TAG]" /> + </actions> + </data> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="delta" ftype="tabular" value="nucmer.txt" /> + <param name="direction" value="False" /> <output name="output" ftype="tabular" compare="diff" value="show-coords.txt" /> </test> + <test expect_num_outputs="1"> + <param name="delta" ftype="tabular" value="nucmer.txt" /> + <param name="direction" value="True" /> + <output name="output_extend" ftype="tabular" compare="diff" value="show-coords_extend.txt" /> + </test> </tests> <help><![CDATA[ This program parses the delta alignment output of nucmer and displays the coordinates, and other useful information about the alignments. -Output is tabular. Below is a description of each column: +Output is tabular. Below is a description of each column (Default): * **[S1]** Start of the alignment region in the reference sequence * **[E1]** End of the alignment region in the reference sequence * **[S2]** Start of the alignment region in the query sequence @@ -61,6 +83,8 @@ Output is tabular. Below is a description of each column: * **[LEN Q]** Length of the query sequence * **[COV R]** Percent coverage of the alignment on the reference sequence, calculated as [LEN 1] / [LEN R] * **[COV Q]** Percent coverage of the alignment on the query sequence, calculated as [LEN 2] / [LEN Q] + * **[FRM R]** Reading frame for the reference sequence (only with -d) + * **[FRM Q]** Reading frame for the query sequence (only with -d) * **[REF TAG]** The reference FastA ID * **[QUERY TAG]** The query FastA ID @@ -72,7 +96,7 @@ The Percent Coverage and Sequence Length options are useful when comparing two s -b Merges overlapping alignments regardless of match dir or frame and does not display any identity information. - + -d Display the alignment direction in the additional FRM columns -I Set minimum percent identity to display -L Set minimum alignment length to display diff --git a/tools/mummer4/test-data/show-coords_extend.txt b/tools/mummer4/test-data/show-coords_extend.txt new file mode 100644 index 00000000000..b3ebd17a143 --- /dev/null +++ b/tools/mummer4/test-data/show-coords_extend.txt @@ -0,0 +1,2 @@ +74 223 43 194 150 152 87.50 6480 5460 2.31 2.78 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5080 5599 4148 4658 520 511 86.18 6480 5460 8.02 9.36 1 1 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724