Mercurial > repos > iuc > progressivemauve
changeset 5:ce795616bd9c draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fcddceef74e33d544e239d1036467f65ef11767f"
| author | iuc |
|---|---|
| date | Sat, 27 Nov 2021 12:13:25 +0000 |
| parents | 4d869208bd52 |
| children | |
| files | progressivemauve.xml test-data/1.backbone |
| diffstat | 2 files changed, 138 insertions(+), 118 deletions(-) [+] |
line wrap: on
line diff
--- a/progressivemauve.xml Wed Oct 13 11:56:19 2021 +0000 +++ b/progressivemauve.xml Sat Nov 27 12:13:25 2021 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="progressivemauve" name="progressiveMauve" version="@WRAPPER_VERSION@.0"> +<tool id="progressivemauve" name="progressiveMauve" version="@WRAPPER_VERSION@.1"> <description>constructs multiple genome alignments</description> <macros> <import>macros.xml</import> @@ -35,6 +35,9 @@ #end if $collinear +#if $input_guide_tree + --input-guide-tree='$input_guide_tree' +#end if --scoring-scheme=$scoring_scheme $no_weight_scaling @@ -50,7 +53,7 @@ #if $gap_open: --gap-open=$gap_open #end if - +--repeat-penalty=$repeat_penalty #if $gap_extend: --gap-extend=$gap_extend #end if @@ -79,7 +82,7 @@ --output-guide-tree=$output_guide_tree_file #end if -#if $output_backbone: +#if $backbone_output: --backbone-output=$output_backbone_file #end if @@ -89,141 +92,144 @@ #end for ]]></command> - <inputs> - <param type="data" format="fasta" name="sequences" multiple="True" - label="Select sequences to align" help="in fasta format" /> - <param type="data" format="xmfa" label="Apply Backbone" name="apply_backbone" optional="True" - help="Read an existing sequence alignment in XMFA format and apply backbone statistics to it (--apply-backbone)" /> + <inputs> + <param type="data" format="fasta" name="sequences" multiple="true" + label="Select sequences to align" help="in fasta format" /> + <param type="data" format="xmfa" label="Apply Backbone" name="apply_backbone" optional="true" + help="Read an existing sequence alignment in XMFA format and apply backbone statistics to it (--apply-backbone)" /> - <param type="integer" label="Island gap size" value="20" name="island_gap_size" - help="Alignment gaps above this size in nucleotides are considered to be islands (--island-gap-size)"/> + <param type="integer" label="Island gap size" value="20" argument="--island-gap-size" + help="Alignment gaps above this size in nucleotides are considered to be islands"/> - <param type="boolean" truevalue="--disable-backbone" falsevalue="" name="disable_backbone" - label="Disable backbone" help="Disable backbone detection (--disable-backbone)" /> + <param type="boolean" truevalue="--disable-backbone" falsevalue="" argument="--disable-backbone" + label="Disable backbone" help="Disable backbone detection" /> - <param type="boolean" truevalue="True" falsevalue="" name="output_guide_tree" - label="Output Guide Tree" help="Write out the guide tree used for alignment to a file (--output-guide-tree)" /> + <param type="boolean" truevalue="true" falsevalue="" argument="--output-guide-tree" + label="Output Guide Tree" help="Write out the guide tree used for alignment to a file" /> - <param type="boolean" truevalue="True" falsevalue="" name="output_backbone" - label="Output Backbone" help="Write out the backbone to a file (--backbone-output)" /> + <param type="boolean" truevalue="true" falsevalue="" argument="--backbone-output" + label="Output Backbone" help="Write out the backbone to a file" /> - <param type="boolean" truevalue="--mums" falsevalue="" label="MUMs" name="mums" - help="Find MUMs only, do not attempt to determine locally collinear blocks (LCBs) (--mums)" /> + <param type="boolean" truevalue="--mums" falsevalue="" label="MUMs" argument="--mums" + help="Find MUMs only, do not attempt to determine locally collinear blocks (LCBs)" /> - <param type="integer" label="Seed weight" name="seed_weight" value="0" optional="True" - help="Use the specified seed weight for calculating initial anchors (--seed-weight)" /> + <param type="integer" label="Seed weight" argument="--seed-weight" value="0" optional="true" + help="Use the specified seed weight for calculating initial anchors" /> - <param type="data" format="tabular" label="Match Input" name="match_input" optional="True" - help="Use specified match file instead of searching for matches (--match-input)" /> + <param type="data" format="tabular" label="Match Input" argument="--match-input" optional="true" + help="Use specified match file instead of searching for matches" /> - <!--<param type="file" label="input-id-matrix" help="An identity matrix describing similarity among all pairs of input sequences/alignments (- -input-id-matrix)" />--> - <param type="integer" label="Max gapped aligner length" value="0" optional="True" name="max_gapped_aligner_length" - help="Maximum number of base pairs to attempt aligning with the gapped aligner (--max-gapped-aligner-length)" /> + <!--<param type="file" label="input-id-matrix" help="An identity matrix describing similarity among all pairs of input sequences/alignments (- -input-id-matrix)" />--> + <param type="integer" label="Max gapped aligner length" value="0" optional="true" argument="--max-gapped-aligner-length" + help="Maximum number of base pairs to attempt aligning with the gapped aligner" /> - <param type="data" format="nhx" label="input-guide-tree" optional="True" name="input_guide_tree" - help="A phylogenetic guide tree in Newick format that describes the order in which sequences will be aligned (--input-guide-tree)" /> + <param type="data" format="nhx" label="input-guide-tree" optional="true" argument="--input-guide-tree" + help="A phylogenetic guide tree in Newick format that describes the order in which sequences will be aligned" /> - <param type="boolean" truevalue="--collinear" falsevalue="" label="Collinear inputs" name="collinear" - help="Assume that input sequences are collinear--they have no rearrangements (--collinear)" /> + <param type="boolean" truevalue="--collinear" falsevalue="" label="Collinear inputs" argument="--collinear" + help="Assume that input sequences are collinear--they have no rearrangements" /> - <param type="select" label="Scoring scheme" name="scoring_scheme" help="Selects the anchoring score function. (--scoring-scheme)" > - <option value="sp" selected="True">Extant sum-of-pairs (sp)</option> - <option value="ancestral_sp">Sum-of-pairs + Ancestral (ancestral_sp)</option> - <option value="ancestral">Ancestral (ancestral)</option> - </param> + <param type="select" label="Scoring scheme" argument="--scoring-scheme" help="Selects the anchoring score function" > + <option value="sp" selected="true">Extant sum-of-pairs (sp)</option> + <option value="ancestral_sp">Sum-of-pairs + Ancestral (ancestral_sp)</option> + <option value="ancestral">Ancestral (ancestral)</option> + </param> - <param type="boolean" truevalue="--no-weight-scaling" falsevalue="" label="No weight scaling" name="no_weight_scaling" - help="Don't scale LCB weights by conservation distance and breakpoint distance (--no-weight-scaling)" /> + <param type="boolean" truevalue="--no-weight-scaling" falsevalue="" label="No weight scaling" argument="--no-weight-scaling" + help="Don't scale LCB weights by conservation distance and breakpoint distance" /> - <param type="float" min="0" max="1" label="max-breakpoint-distance-scale" value="0.5" name="max_breakpoint_distance_scale" - help="Set the maximum weight scaling by breakpoint distance. (--max-breakpoint-distance-scale)" /> + <param type="float" min="0" max="1" label="max-breakpoint-distance-scale" value="0.5" argument="--max-breakpoint-distance-scale" + help="Set the maximum weight scaling by breakpoint distance" /> - <param type="float" min="0" max="1" label="conservation-distance-scale" value="0.5" name="conservation_distance_scale" - help="Scale conservation distances by this amount. (--conservation-distance-scale)" /> + <param type="float" min="0" max="1" label="conservation-distance-scale" value="0.5" argument="--conservation-distance-scale" + help="Scale conservation distances by this amount" /> - <param type="boolean" truevalue="--skip-refinement" falsevalue="" label="Skip refinement" name="skip_refinement" - help="Do not perform iterative refinement (--skip-refinement)" /> - <param type="boolean" truevalue="--skip-gapped-alignment" falsevalue="" label="Skip gapped alignment" name="skip_gapped_alignment" - help="Do not perform gapped alignment (--skip-gapped-alignment)" /> - <param type="integer" label="BP dist estimate min score" name="bp_dist_estimate_min_score" value="0" optional="True" - help="Minimum LCB score for estimating pairwise breakpoint distance (--bp-dist-estimate-min-score)" /> + <param type="boolean" truevalue="--skip-refinement" falsevalue="" label="Skip refinement" argument="--skip-refinement" + help="Do not perform iterative refinement" /> + <param type="boolean" truevalue="--skip-gapped-alignment" falsevalue="" label="Skip gapped alignment" argument="--skip-gapped-alignment" + help="Do not perform gapped alignment" /> + <param type="integer" label="BP dist estimate min score" argument="--bp-dist-estimate-min-score" value="0" optional="true" + help="Minimum LCB score for estimating pairwise breakpoint distance" /> - <param type="integer" label="Gap open" name="gap_open" value="0" optional="True" - help="Gap open penalty (--gap-open)" /> + <param type="integer" label="Gap open" argument="--gap-open" value="0" optional="true" + help="Gap open penalty" /> - <param type="select" label="Repeat penalty" name="repeat_penalty" - help="Sets whether the repeat scores go negative or go to zero for highly repetitive sequences. (--repeat-penalty)"> - <option value="negative" selected="True">Negative</option> - <option value="zero">Zero</option> - </param> + <param type="select" label="Repeat penalty" argument="--repeat-penalty" + help="Sets whether the repeat scores go negative or go to zero for highly repetitive sequences"> + <option value="negative" selected="true">Negative</option> + <option value="zero">Zero</option> + </param> - <param type="integer" label="Gap extend" name="gap_extend" value="0" optional="True" - help="Gap extend penalty (--gap-extend)" /> + <param type="integer" label="Gap extend" argument="--gap-extend" value="0" optional="true" + help="Gap extend penalty" /> - <!--<param type="data" label="Substitution matrix" --> - <!--help="Nucleotide substitution matrix in NCBI format (- -substitution-matrix)" />--> + <!--<param type="data" label="Substitution matrix" --> + <!--help="Nucleotide substitution matrix in NCBI format (- -substitution-matrix)" />--> - <param type="integer" label="Weight" name="weight" value="0" optional="True" - help="Minimum pairwise LCB score (--weight)" /> - <param type="integer" label="Min scaled penalty" name="min_scaled_penalty" value="0" optional="True" - help="Minimum breakpoint penalty after scaling the penalty by expected divergence (--min-scaled-penalty)" /> + <param type="integer" label="Weight" argument="--weight" value="0" optional="true" + help="Minimum pairwise LCB score" /> + <param type="integer" label="Min scaled penalty" argument="--min-scaled-penalty" value="0" optional="true" + help="Minimum breakpoint penalty after scaling the penalty by expected divergence" /> - <param type="float" label="HMM p go homologous" name="hmm_p_go_homologous" min="0" max="1" value="0.00001" - help="Probability of transitioning from the unrelated to the homologous state (--hmm-p-go-homologous)" /> - <param type="float" label="HMM p go unrelated" name="hmm_p_go_unrelated" min="0" max="1" value="0.000000001" - help="Probability of transitioning from the homologous to the unrelated state (--hmm-p-go-unrelated)" /> - <param type="float" label="HMM identity" name="hmm_identity" min="0" max="1" value="0.7" - help="Expected level of sequence identity among pairs of sequences(--hmm-identity)" /> + <param type="float" label="HMM p go homologous" argument="--hmm-p-go-homologous" min="0" max="1" value="0.00001" + help="Probability of transitioning from the unrelated to the homologous state" /> + <param type="float" label="HMM p go unrelated" argument="--hmm-p-go-unrelated" min="0" max="1" value="0.000000001" + help="Probability of transitioning from the homologous to the unrelated state" /> + <param type="float" label="HMM identity" argument="--hmm-identity" min="0" max="1" value="0.7" + help="Expected level of sequence identity among pairs of sequences" /> - <param type="boolean" truevalue="--seed-family" falsevalue="" label="Seed family" name="seed_family" - help="Use a family of spaced seeds to improve sensitivity (--seed-family)" /> - <param type="boolean" truevalue="--solid-seeds" falsevalue="" label="Solid seeds" name="solid_seeds" - help="Use solid seeds. Do not permit substitutions in anchor matches. (--solid-seeds)" /> - <param type="boolean" truevalue="--coding-seeds" falsevalue="" label="Coding seeds" name="coding_seeds" - help="Use coding pattern seeds. Useful to generate matches coding regions with 3rd codon position degeneracy. (--coding-seeds)" /> - <param type="boolean" truevalue="--no-recursion" falsevalue="" label="No recursion" name="no_recursion" - help="Disable recursive anchor search (--no-recursion)" /> - </inputs> - <outputs> - <data format="xmfa" name="output" label="${tool.name} alignment of ${on_string}"> - <change_format> - <when input="mums" value="--mums" format="tabular" /> - </change_format> - </data> - <data format="nhx" name="output_guide_tree_file" label="${tool.name} alignment of ${on_string}: Guide tree"> - <filter>output_guide_tree</filter> - </data> - <data format="tabular" name="output_backbone_file" label="${tool.name} alignment of ${on_string}: Backbone"> - <filter>output_backbone</filter> - </data> - </outputs> - <tests> - <test> - <param name="sequences" value="phagey.fa,karma.fa" /> - <output name="output" file="1.xmfa" lines_diff="20"/> - </test> - <test> - <param name="sequences" value="merged.fa" /> - <output name="output" file="2.xmfa" lines_diff="20"/> - </test> - <test> - <param name="sequences" value="merged.fa" /> - <param name="output_guide_tree" value="True" /> - <output name="output" file="2.xmfa" lines_diff="20"/> - <output name="output_guide_tree_file" file="1.nhx" /> - </test> - <test> - <param name="sequences" value="merged.fa" /> - <param name="mums" value="True" /> - <output name="output" file="1.mums" compare="sim_size" delta="1000"/> - </test> - <test> - <param name="sequences" value="merged.fa" /> - <param name="match_input" value="1.mums" ftype="tabular"/> - <output name="output" file="2.xmfa" lines_diff="24"/> - </test> - </tests> - <help><![CDATA[ + <param type="boolean" truevalue="--seed-family" falsevalue="" label="Seed family" argument="--seed-family" + help="Use a family of spaced seeds to improve sensitivity" /> + <param type="boolean" truevalue="--solid-seeds" falsevalue="" label="Solid seeds" argument="--solid-seeds" + help="Use solid seeds. Do not permit substitutions in anchor matches" /> + <param type="boolean" truevalue="--coding-seeds" falsevalue="" label="Coding seeds" argument="--coding-seeds" + help="Use coding pattern seeds. Useful to generate matches coding regions with 3rd codon position degeneracy" /> + <param type="boolean" truevalue="--no-recursion" falsevalue="" label="No recursion" argument="--no-recursion" + help="Disable recursive anchor search" /> + </inputs> + <outputs> + <data format="xmfa" name="output" label="${tool.name} alignment of ${on_string}"> + <change_format> + <when input="mums" value="--mums" format="tabular" /> + </change_format> + </data> + <data format="nhx" name="output_guide_tree_file" label="${tool.name} alignment of ${on_string}: Guide tree"> + <filter>output_guide_tree and not mums</filter> + </data> + <data format="tabular" name="output_backbone_file" label="${tool.name} alignment of ${on_string}: Backbone"> + <filter>backbone_output and not mums</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="sequences" value="phagey.fa,karma.fa" /> + <output name="output" file="1.xmfa" lines_diff="20" ftype="xmfa"/> + </test> + <test expect_num_outputs="1"> + <param name="sequences" value="merged.fa" /> + <output name="output" file="2.xmfa" lines_diff="20" ftype="xmfa"/> + </test> + <test expect_num_outputs="3"> + <param name="sequences" value="merged.fa" /> + <param name="output_guide_tree" value="true" /> + <param name="backbone_output" value="true" /> + <output name="output" file="2.xmfa" lines_diff="20" ftype="xmfa"/> + <output name="output_guide_tree_file" file="1.nhx" /> + <output name="output_backbone_file" file="1.backbone" /> + </test> + <test expect_num_outputs="1"> + <param name="sequences" value="merged.fa" /> + <param name="output_guide_tree" value="true" /> + <param name="mums" value="true" /> + <output name="output" file="1.mums" compare="sim_size" delta="1000" ftype="tabular"/> + </test> + <test expect_num_outputs="1"> + <param name="sequences" value="merged.fa" /> + <param name="match_input" value="1.mums" ftype="tabular"/> + <output name="output" file="2.xmfa" lines_diff="24" ftype="xmfa"/> + </test> + </tests> + <help><![CDATA[ What it does ============ @@ -434,6 +440,6 @@ the command line, you'll need to pass these flags with their "default" values. @ATTRIBUTION@ -]]></help> - <expand macro="citation" /> + ]]></help> + <expand macro="citation" /> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.backbone Sat Nov 27 12:13:25 2021 +0000 @@ -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