| Previous changeset 4:4d869208bd52 (2021-10-13) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fcddceef74e33d544e239d1036467f65ef11767f" |
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modified:
progressivemauve.xml |
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added:
test-data/1.backbone |
| b |
| diff -r 4d869208bd52 -r ce795616bd9c progressivemauve.xml --- a/progressivemauve.xml Wed Oct 13 11:56:19 2021 +0000 +++ b/progressivemauve.xml Sat Nov 27 12:13:25 2021 +0000 |
| [ |
| b'@@ -1,5 +1,5 @@\n <?xml version="1.0"?>\n-<tool id="progressivemauve" name="progressiveMauve" version="@WRAPPER_VERSION@.0">\n+<tool id="progressivemauve" name="progressiveMauve" version="@WRAPPER_VERSION@.1">\n <description>constructs multiple genome alignments</description>\n <macros>\n <import>macros.xml</import>\n@@ -35,6 +35,9 @@\n #end if\n \n $collinear\n+#if $input_guide_tree\n+ --input-guide-tree=\'$input_guide_tree\'\n+#end if\n --scoring-scheme=$scoring_scheme\n $no_weight_scaling\n \n@@ -50,7 +53,7 @@\n #if $gap_open:\n --gap-open=$gap_open\n #end if\n-\n+--repeat-penalty=$repeat_penalty\n #if $gap_extend:\n --gap-extend=$gap_extend\n #end if\n@@ -79,7 +82,7 @@\n --output-guide-tree=$output_guide_tree_file\n #end if\n \n-#if $output_backbone:\n+#if $backbone_output:\n --backbone-output=$output_backbone_file\n #end if\n \n@@ -89,141 +92,144 @@\n #end for\n \n ]]></command>\n- <inputs>\n- <param type="data" format="fasta" name="sequences" multiple="True"\n- label="Select sequences to align" help="in fasta format" />\n- <param type="data" format="xmfa" label="Apply Backbone" name="apply_backbone" optional="True"\n- help="Read an existing sequence alignment in XMFA format and apply backbone statistics to it (--apply-backbone)" />\n+ <inputs>\n+ <param type="data" format="fasta" name="sequences" multiple="true"\n+ label="Select sequences to align" help="in fasta format" />\n+ <param type="data" format="xmfa" label="Apply Backbone" name="apply_backbone" optional="true"\n+ help="Read an existing sequence alignment in XMFA format and apply backbone statistics to it (--apply-backbone)" />\n \n- <param type="integer" label="Island gap size" value="20" name="island_gap_size"\n- help="Alignment gaps above this size in nucleotides are considered to be islands (--island-gap-size)"/>\n+ <param type="integer" label="Island gap size" value="20" argument="--island-gap-size"\n+ help="Alignment gaps above this size in nucleotides are considered to be islands"/>\n \n- <param type="boolean" truevalue="--disable-backbone" falsevalue="" name="disable_backbone"\n- label="Disable backbone" help="Disable backbone detection (--disable-backbone)" />\n+ <param type="boolean" truevalue="--disable-backbone" falsevalue="" argument="--disable-backbone"\n+ label="Disable backbone" help="Disable backbone detection" />\n \n- <param type="boolean" truevalue="True" falsevalue="" name="output_guide_tree"\n- label="Output Guide Tree" help="Write out the guide tree used for alignment to a file (--output-guide-tree)" />\n+ <param type="boolean" truevalue="true" falsevalue="" argument="--output-guide-tree"\n+ label="Output Guide Tree" help="Write out the guide tree used for alignment to a file" />\n \n- <param type="boolean" truevalue="True" falsevalue="" name="output_backbone"\n- label="Output Backbone" help="Write out the backbone to a file (--backbone-output)" />\n+ <param type="boolean" truevalue="true" falsevalue="" argument="--backbone-output"\n+ label="Output Backbone" help="Write out the backbone to a file" />\n \n- <param type="boolean" truevalue="--mums" falsevalue="" label="MUMs" name="mums"\n- help="Find MUMs only, do not attempt to determine locally collinear blocks (LCBs) (--mums)" />\n+ <param type="boolean" truevalue="--mums" falsevalue="" label="MUMs" argument="--mums"\n+ help="Find MUMs only, do not attempt to determine locally collinear blocks (LCBs)" />\n \n- <param type="integer" label="Seed weight" name="seed_weight" value="0" optional="True"\n- help="Use the specified seed weight for calculating initial anchors (--seed-weight)" />\n+ <param type="integer" label="Seed weight" argument="--seed-weight" value="0" optional="true"\n+ help="Use the specified seed weight for calculating initial anchors" />\n \n- <param type="data" forma'..b'file="2.xmfa" lines_diff="20"/>\n- </test>\n- <test>\n- <param name="sequences" value="merged.fa" />\n- <param name="output_guide_tree" value="True" />\n- <output name="output" file="2.xmfa" lines_diff="20"/>\n- <output name="output_guide_tree_file" file="1.nhx" />\n- </test>\n- <test>\n- <param name="sequences" value="merged.fa" />\n- <param name="mums" value="True" />\n- <output name="output" file="1.mums" compare="sim_size" delta="1000"/>\n- </test>\n- <test>\n- <param name="sequences" value="merged.fa" />\n- <param name="match_input" value="1.mums" ftype="tabular"/>\n- <output name="output" file="2.xmfa" lines_diff="24"/>\n- </test>\n- </tests>\n- <help><![CDATA[\n+ <param type="boolean" truevalue="--seed-family" falsevalue="" label="Seed family" argument="--seed-family"\n+ help="Use a family of spaced seeds to improve sensitivity" />\n+ <param type="boolean" truevalue="--solid-seeds" falsevalue="" label="Solid seeds" argument="--solid-seeds"\n+ help="Use solid seeds. Do not permit substitutions in anchor matches" />\n+ <param type="boolean" truevalue="--coding-seeds" falsevalue="" label="Coding seeds" argument="--coding-seeds"\n+ help="Use coding pattern seeds. Useful to generate matches coding regions with 3rd codon position degeneracy" />\n+ <param type="boolean" truevalue="--no-recursion" falsevalue="" label="No recursion" argument="--no-recursion"\n+ help="Disable recursive anchor search" />\n+ </inputs>\n+ <outputs>\n+ <data format="xmfa" name="output" label="${tool.name} alignment of ${on_string}">\n+ <change_format>\n+ <when input="mums" value="--mums" format="tabular" />\n+ </change_format>\n+ </data>\n+ <data format="nhx" name="output_guide_tree_file" label="${tool.name} alignment of ${on_string}: Guide tree">\n+ <filter>output_guide_tree and not mums</filter>\n+ </data>\n+ <data format="tabular" name="output_backbone_file" label="${tool.name} alignment of ${on_string}: Backbone">\n+ <filter>backbone_output and not mums</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test expect_num_outputs="1">\n+ <param name="sequences" value="phagey.fa,karma.fa" />\n+ <output name="output" file="1.xmfa" lines_diff="20" ftype="xmfa"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="sequences" value="merged.fa" />\n+ <output name="output" file="2.xmfa" lines_diff="20" ftype="xmfa"/>\n+ </test>\n+ <test expect_num_outputs="3">\n+ <param name="sequences" value="merged.fa" />\n+ <param name="output_guide_tree" value="true" />\n+ <param name="backbone_output" value="true" />\n+ <output name="output" file="2.xmfa" lines_diff="20" ftype="xmfa"/>\n+ <output name="output_guide_tree_file" file="1.nhx" />\n+ <output name="output_backbone_file" file="1.backbone" />\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="sequences" value="merged.fa" />\n+ <param name="output_guide_tree" value="true" />\n+ <param name="mums" value="true" />\n+ <output name="output" file="1.mums" compare="sim_size" delta="1000" ftype="tabular"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="sequences" value="merged.fa" />\n+ <param name="match_input" value="1.mums" ftype="tabular"/>\n+ <output name="output" file="2.xmfa" lines_diff="24" ftype="xmfa"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n What it does\n ============\n \n@@ -434,6 +440,6 @@\n the command line, you\'ll need to pass these flags with their "default" values.\n \n @ATTRIBUTION@\n-]]></help>\n- <expand macro="citation" />\n+ ]]></help>\n+ <expand macro="citation" />\n </tool>\n' |
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| diff -r 4d869208bd52 -r ce795616bd9c test-data/1.backbone --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.backbone Sat Nov 27 12:13:25 2021 +0000 |
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| @@ -0,0 +1,14 @@ +seq0_leftend seq0_rightend seq1_leftend seq1_rightend +-149367 -149557 61896 62084 +-146933 -147092 64840 65002 +-146188 -146438 65643 65884 +-140708 -140920 81644 81870 +-83043 -83153 118757 118870 +83154 140707 0 0 +140921 146187 0 0 +146439 146932 0 0 +147093 149366 0 0 +0 0 62085 64839 +0 0 65003 65642 +0 0 65885 81643 +0 0 81871 118756 |