diff progressivemauve.xml @ 1:bd1901839519 draft

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/progressivemauve.xml	Mon Jun 05 02:46:06 2023 +0000
@@ -0,0 +1,262 @@
+<tool id="progressivemauve" name="progressiveMauve" version="19.1.0.0" profile="16.04">
+    <description>constructs multiple genome alignments</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>cpt-macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package">progressivemauve</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+## Symlink files in with correct extensions
+#for $file in '$sequences':
+    ln -s '$file' `basename '$file'`;
+#end for
+
+progressiveMauve
+## Input Options
+
+#if $apply_backbone:
+    --apply-backbone='$apply_backbone'
+#end if
+--island-gap-size='$island_gap_size'
+'$mums'
+
+#if $seed_weight:
+    --seed-weight='$seed_weight'
+#end if
+
+#if $max_gapped_aligner_length:
+    --max-gapped-aligner-length='$max_gapped_aligner_length'
+#end if
+
+#if $match_input:
+    --match-input='$match_input'
+#end if
+
+'$collinear'
+--scoring-scheme='$scoring_scheme'
+'$no_weight_scaling'
+
+--max-breakpoint-distance-scale='$max_breakpoint_distance_scale'
+--conservation-distance-scale='$conservation_distance_scale'
+'$skip_refinement'
+'$skip_gapped_alignment'
+
+#if $bp_dist_estimate_min_score:
+    --bp-dist-estimate-min-score='$bp_dist_estimate_min_score'
+#end if
+
+#if $gap_open:
+    --gap-open='$gap_open'
+#end if
+
+#if $gap_extend:
+    --gap-extend='$gap_extend'
+#end if
+
+#if $weight:
+    --weight='$weight'
+#end if
+
+#if $min_scaled_penalty:
+    --min-scaled-penalty='$min_scaled_penalty'
+#end if
+
+--hmm-p-go-homologous='$hmm_p_go_homologous'
+--hmm-p-go-unrelated='$hmm_p_go_unrelated'
+--hmm-identity='$hmm_identity'
+
+'$seed_family'
+'$solid_seeds'
+'$coding_seeds'
+'$no_recursion'
+'$disable_backbone'
+
+## Outputs
+--output='$output'
+#if $output_guide_tree:
+    --output-guide-tree='$output_guide_tree_file'
+#end if
+
+#if $output_backbone:
+    --backbone-output='$output_backbone_file'
+#end if
+
+## Sequences
+#for file in $sequences:
+    `basename "${file}"`
+#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)"/>
+        <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="boolean" truevalue="--disable-backbone" falsevalue="" name="disable_backbone" label="Disable backbone" help="Disable backbone detection (--disable-backbone)"/>
+        <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="" name="output_backbone" label="Output Backbone" help="Write out the backbone to a file (--backbone-output)"/>
+        <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="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="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="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="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="boolean" truevalue="--collinear" falsevalue="" label="Collinear inputs" name="collinear" help="Assume that input sequences are collinear--they have no rearrangements (--collinear)"/>
+        <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="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="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="conservation-distance-scale" value="0.5" name="conservation_distance_scale" help="Scale conservation distances by this amount. (--conservation-distance-scale)"/>
+        <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="integer" label="Gap open" name="gap_open" value="0" optional="True" help="Gap open penalty (--gap-open)"/>
+        <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="integer" label="Gap extend" name="gap_extend" value="0" optional="True" help="Gap extend penalty (--gap-extend)"/>
+        <!--<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="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="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="3.xmfa" lines_diff="20"/>
+            <output name="output_guide_tree_file" file="3.nhx"/>
+        </test>
+        <test>
+            <param name="sequences" value="merged.fa"/>
+            <param name="mums" value="True"/>
+            <output name="output" file="4.mums" compare="sim_size" delta="1000"/>
+        </test>
+        <test>
+            <param name="sequences" value="merged.fa"/>
+            <param name="match_input" value="4.mums"/>
+            <output name="output" file="5.xmfa" lines_diff="24"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+What it does
+============
+
+Mauve is a system for efficiently constructing multiple genome alignments in
+the presence of large-scale evolutionary events such as rearrangement and
+inversion. Multiple genome alignment provides a basis for research into
+comparative genomics and the study of evolutionary dynamics. Aligning whole
+genomes is a fundamentally different problem than aligning short sequences.
+
+Mauve has been developed with the idea that a multiple genome aligner should
+require only modest computational resources. It employs algorithmic techniques
+that scale well in the amount of sequence being aligned. For example, a pair of
+Y. pestis genomes can be aligned in under a minute, while a group of 9
+divergent Enterobacterial genomes can be aligned in a few hours.
+
+
+Example Usage
+=============
+
++-----------------------------------+-------------+
+| Usage                             | Notes       |
++===================================+=============+
+| Align genomes                     |Simply       |
+|                                   |select as    |
+|                                   |many fasta   |
+|                                   |files with   |
+|                                   |one or more  |
+|                                   |sequences as |
+|                                   |necessary    |
++-----------------------------------+-------------+
+| Align genomes but also save       |Use the      |
+| the guide tree and produce a      |**Output     |
+| backbone file                     |Guide Tree** |
+|                                   |and **Output |
+|                                   |Backbone**   |
+|                                   |options      |
++-----------------------------------+-------------+
+| Align genomes, but do not         |Use the      |
+| detect forced alignment of        |**Disable    |
+| unrelated sequences               |backbone**   |
+|                                   |option       |
++-----------------------------------+-------------+
+| Detect forced alignment of        |Use the      |
+| unrelated sequence in the         |**Apply      |
+| alignment produced                |Backbone**   |
+| in previous example, use          |option and   |
+| custom Homology HMM transition    |specify the  |
+| parameters.                       |XMFA file    |
+|                                   |produced     |
+|                                   |in the       |
+|                                   |previous     |
+|                                   |example      |
++-----------------------------------+-------------+
+| Compute ungapped                  |Use the      |
+| local-multiple alignments among   |**MUMs**     |
+| the input sequences               |option       |
++-----------------------------------+-------------+
+| Compute an alignment of the       |Set the      |
+| same genomes, using previously    |**Match      |
+| computed local-multiple           |Input** to   |
+| alignments                        |the tabular  |
+|                                   |MUMs file    |
+|                                   |produced in  |
+|                                   |the previous |
+|                                   |example      |
++-----------------------------------+-------------+
+| Set a minimum scaled              |Use the      |
+| breakpoint penalty to cope with   |**Min Scaled |
+| the case where most genomes       |Penalty** and|
+| are aligned correctly, but manual |set to a     |
+| inspection reveals that           |value like   |
+| a divergent genome has too        |5000         |
+| many predicted rearrangements.    |             |
++-----------------------------------+-------------+
+| Globally align a set of           |Use the      |
+| collinear virus                   |**Colinear**,|
+| genomes, using seed families      |**Seed       |
+| to improve anchoring sensitivity  |Family**     |
+| in regions below 70% sequence     |options      |
+| identity.                         |             |
++-----------------------------------+-------------+
+
+]]></help>
+    <citations>
+        <expand macro="citation/progressive_mauve"/>
+        <expand macro="citation/mijalisrasche"/>
+    </citations>
+</tool>