Add carveme

tools/carveme/.shed.yml

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+name: carveme
+owner: bgruening
+long_description: CarveMe is a tool to reconstruct genome scale metabolic models
+homepage_url: https://github.com/cdanielmachado/carveme
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/carveme
+description: Genome-scale metabolic model reconstruction with CarveMe
+categories:
+- Systems Biology

tools/carveme/carveme.xml

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+<tool id="carveme" name="CarveMe" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Tool to reconstruct genome-scale metabolic models</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.6.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <xml name="biotools">
+            <xrefs>
+                <xref type="bio.tools">CarveMe</xref>
+            </xrefs>
+        </xml>
+    </macros>
+    <requirements>
+        <requirement type='package' version="@TOOL_VERSION@">carveme</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    carve '$annotation'
+    #if $dna
+        --dna
+    #end if
+    #if $egg
+        --egg 
+    #end if
+    #if $fc2
+        --fc2 
+    #end if
+    #if $cobra
+        --cobra 
+    #end if
+    #if $diamond_args
+        --diamond-args '$diamond_args'
+    #end if
+    #if $universe
+        --universe '$universe'
+    #end if 
+    #if $universe_file
+        --universe-file '$universe_file'
+    #end if
+    #if $mediadb
+        --mediadb '$mediadb'
+    #end if
+    #if $soft
+        --soft '$soft'
+    #end if
+    #if $hard
+        --hard '$hard'
+    #end if
+    #if $reference
+        --reference '$reference'
+    #end if
+    --solver scip
+    --output '$model'
+    ]]></command>
+    <inputs>
+    <param name="annotation" label="Annotation file" type="data" format="text" optional="false" multiple="false"/>
+    <param argument="--dna" label="Build from DNA FASTA file" type="boolean" truevalue="--dna" falsevalue="" optional="true"/>
+    <param argument="--egg" label="Build from eggNOG-mapper annotation file" type="boolean" truevalue="--egg" falsevalue="" optional="true"/>
+    <param argument="--fc2" label="Output SBML in sbml-fbc2 format" type="boolean" truevalue="--fc2" falsevalue="" optional="true"/>
+    <param argument="--universe" label="Pre-built universe model (default: Bacteria)" type="select" optional="true" multiple="false">
+        <option value="grampos">Gram Positive</option>
+        <option value="gramneg">Gram Negative</option>
+        <option value="cyanobacteria">Cyanobacteria</option>
+        <option value="archaea">Archaea</option>
+    </param>
+    <param argument="--cobra" label="Output SBML in old cobra format" type="boolean" truevalue="--cobra" falsevalue="" optional="true"/>
+    <param argument="--diamond-args" label="Additional arguments for running diamond"  type="text" optional="true"/>
+    <param argument="--universe-file" label="Reaction universe file (SBML format)"  type="data" format="sbml" optional="true"/>
+    <param argument="--mediadb" label="Media database file" type="data" format="tsv" optional="true"/>
+    <param argument="--soft" label="Soft constraints file" type="data" format="tsv" optional="true"/>
+    <param argument="--hard" label="Hard constraints file" type="data" format="tsv" optional="true"/>
+    <param argument="--reference" type="data" format="sbml" optional="true" label="Manually curated model of a close reference species"/>
+    </inputs>
+    <outputs>
+        <data name="model" format="xml"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="annotation" value="protein.faa"/>
+            <param name="universe_file" value="e_coli_core.xml"/>
+            <output name="model" value="modeltest.xml" ftype='xml' />
+        </test>
+    </tests>
+    <help>
+
+CarveMe reconstructs genome-scale metabolic models of prokaryotes using an annotated genome to 'carve' a universal model.
+
+An annotation input is required as a protein or DNA FASTA file, or, as an eggNOG output.
+
+The default universe is 'bacteria', but alternative, more specific, universes are available for Gram-Positive/Negative, Cyanobacteria and Archaea.
+
+Other universes might be uploaded by the user (e.g. for yeast reconstructions).
+
+Providing a Media database file enforces the model to grow in the said media.
+
+Reactions' directionalities (1:forward, -1:backward, 0:blocked) can be enforced with a soft constraints tabular file:  (e.g R_XXX    -1).
+
+Reactions' bounds can be enforced with a hard constraints tabular file (e.g. R_XXX      -10     10)
+
+
+Note: Different solvers may result in slightly different models. 
+Here, the reconstructions rely on the open source solver SCIP. 
+For local installations, CPLEX or Gurobi are faster alternatives.
+
+    </help>
+    <citations>
+        <citation type="doi">10.1093/nar/gky537</citation>
+    </citations>    
+</tool>