diff apoc.xml @ 0:67d2a6f3b4e3 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ commit d25418e6fe5eddd1a1cc68979e5898fb224feffe

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/apoc.xml	Fri Jul 07 11:35:29 2017 -0400
@@ -0,0 +1,191 @@
+<tool id="apoc" name="APoc" version="1.0">
+    <description>Large-scale identification of similar protein pockets</description>
+    <requirements>
+        <requirement type="package" version="1b16">apoc</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+#if $templates_source.template_source_select == 'list'
+    #for $i, $s in enumerate( $templates_source.template )
+        echo '${s.input.file_name}' >> templates_path &&
+    #end for#
+    paste -d "\t" templates_path '$templates_source.lt' | awk '{print $1"\t"$3}' > templates_list &&
+#end if#
+
+#if $query_source.query_source_select == 'list'
+    #for $i, $s in enumerate( $query_source.query )
+        echo '${s.input.file_name}' >> queries_path &&
+    #end for#
+    paste -d "\t" queries_path '$query_source.lq' | awk '{print $1"\t"$3}' > queries_list &&
+#end if#
+
+apoc
+-fa $fa
+-pvol $pvol
+-plen $plen
+$alignment_option.sod
+-v $alignment_option.v
+-m $scoring_option.m
+#if str($scoring_option.L)
+    -L $scoring_option.L
+#end if
+$scoring_option.a
+$scoring_option.b
+$scoring_option.c
+
+#if $templates_source.template_source_select == 'list'
+    -lt templates_list
+#else
+    #if $templates_source.pt
+        -pt '$templates_source.pt'
+    #end if
+    '$templates_source.pdbfile1'
+#end if
+
+#if $query_source.query_source_select == 'list'
+    -lq queries_list
+#else
+    #if $query_source.pq
+        -pq '$query_source.pq'
+    #end if
+    '$query_source.pdbfile2'
+#end if
+> $output_apoc
+    ]]></command>
+    <inputs>
+        <conditional name="templates_source">
+            <param name="template_source_select" type="select" label="Chose template source: pdb file or file with list of templates">
+                <option value="pdbfile">pdb file</option>
+                <option value="list">file with list of templates</option>
+            </param>
+            <when value="pdbfile">
+                <param name="pdbfile1" type="data" format="pdb" label="First (template) structure for comparison" />
+                <param argument="-pt" type="text" label="Names of pockets in the first (template) structure for comparison" optional="true" />
+            </when>
+            <when value="list">
+                <param argument="-lt" type="data" format="data" label="List of templates to compare in a file" />
+                <repeat name="template" title="pdb file from list of templates">
+                    <param name="input" type="data" format="pdb" label="pdbfile" help="Load all pdb files in the same order as in the list of templates" />
+                </repeat>
+            </when>
+        </conditional>
+        <conditional name="query_source">
+            <param name="query_source_select" type="select" label="Chose query source: pdb file or file with list of queries">
+                <option value="pdbfile">pdb file </option>
+                <option value="list">file with list of queries</option>
+            </param>
+            <when value="pdbfile">
+                <param name="pdbfile2" type="data" format="pdb" label="Second (query) structure for comparison" />
+                <param argument="-pq" type="text" optional="true" label="Names of pockets in the second (query) structure for comparison" />
+            </when>
+            <when value="list">
+                <param argument="-lq" type="data" format="data" label="List of queries (targets) to compare in a file." />
+                <repeat name="query" title="pdb file from list of queries">
+                    <param name="input" type="data" format="pdb" label="pdbfile" help="Load all pdb files in the same order as in the list of queries" />
+                </repeat>
+            </when>
+        </conditional>
+        <param argument="-fa" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Global structure alignment" />
+        <param argument="-pvol" type="integer" value="1000" label="Minimal pocket volume in grid points" />
+        <param argument="-plen" type="integer" value="10" label="Minimal number of pocket residues" />
+        <section name="alignment_option" title="Alignment option">
+            <param argument="-sod" type="boolean" truevalue="-sod" falsevalue="" label="Restrict to sequence-order-dependent alignment" />
+            <param argument="-v" type="select" label="Restrict to sequence-order-dependent alignment" >
+                <option value="0">None</option>
+                <option value="1">Concise</option>
+                <option value="2" selected="true">Detailed</option>
+            </param>
+        </section>
+        <section name="scoring_option" title="Scoring option">
+            <param argument="-m" type="select" label="Similarity scoring metric" >
+                <option value="tm">TM-score</option>
+                <option value="ps" selected="true">PS-score</option>
+            </param>
+            <param argument="-L" type="integer" optional="true" label="Normalize the score with this fixed length" />
+            <param argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Normalize the score by the average size of two structures" />
+            <param argument="-b" type="boolean" truevalue="-b" falsevalue="" label="Normalize the score by the minimum size of two structures" />
+            <param argument="-c" type="boolean" truevalue="-c" falsevalue="" label="Normalize the score by the maximum size of two structures" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output_apoc" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="template_source_select" value="pdbfile" />
+            <param name="pdbfile1" value="apoc/1ha3A.pdb" ftype="pdb" />
+            <param name="query_source_select" value="pdbfile" />
+            <param name="pdbfile2" value="apoc/3ec1A.pdb" ftype="pdb" />
+            <output name="output_apoc">
+                <assert_contents>
+                    <has_text_matching expression="PDB\s*files\s*loaded" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="template_source_select" value="list" />
+            <param name="lt" value="apoc/templ.lst" />
+            <param name="template_0|input" value="apoc/1ha3A.pdb" ftype="pdb" />
+            <param name="template_1|input" value="apoc/3ec1A.pdb" ftype="pdb" />
+            <param name="template_2|input" value="apoc/1yr8A.pdb" ftype="pdb" />
+            <param name="query_source_select" value="pdbfile" />
+            <param name="pdbfile2" value="apoc/1yr8A.pdb" ftype="pdb" />
+            <output name="output_apoc">
+                <assert_contents>
+                    <has_text_matching expression="PDB\s*files\s*loaded" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="template_source_select" value="list" />
+            <param name="lt" value="apoc/templ.lst" />
+            <param name="template_0|input" value="apoc/1ha3A.pdb" ftype="pdb" />
+            <param name="template_1|input" value="apoc/3ec1A.pdb" ftype="pdb" />
+            <param name="template_2|input" value="apoc/1yr8A.pdb" ftype="pdb" />
+            <param name="query_source_select" value="pdbfile" />
+            <param name="pdbfile2" value="apoc/1ha3A.pdb" ftype="pdb" />
+            <param name="pq" value="1ha3_GDP_A_406" />
+            <output name="output_apoc">
+                <assert_contents>
+                    <has_text_matching expression="PDB\s*files\s*loaded" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="template_source_select" value="list" />
+            <param name="lt" value="apoc/templ.lst" />
+            <param name="template_0|input" value="apoc/1ha3A.pdb" ftype="pdb" />
+            <param name="template_1|input" value="apoc/3ec1A.pdb" ftype="pdb" />
+            <param name="template_2|input" value="apoc/1yr8A.pdb" ftype="pdb" />
+            <param name="query_source_select" value="list" />
+            <param name="lq" value="apoc/query.lst" />
+            <param name="query_0|input" value="apoc/3ec1A.pdb" ftype="pdb" />
+            <output name="output_apoc">
+                <assert_contents>
+                    <has_text_matching expression="PDB\s*files\s*loaded" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+***********
+Description
+***********
+
+APoc may be used to compare two pockets, a pocket against a set of pockets, or
+all-against-all between two sets of pockets. If you supply two structures to compare,
+the first structure is the template and the second structure is the query (or target).
+
+For each pair of structures, the program first performs a global structural comparison in
+sequential order using a standard TM-align algoritm. One may elect to bypass the global alignment
+to accelerate comparison. If no pocket found in the pdb structures, the program becomes a normal
+TM-align or stop if one chooses to bypass the global alignment. If there are pockets detected
+in the input files, it will compare pockets in sequential-order-independent manner by default.
+
+The ouput is arranged in pairs of structures compared. For each pair, the first alignment is the
+global alignment, followed by all-againat-all alignment of selected pockets. If you want a concise
+output without detailed alignment, add the "-v 0" option.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btt024</citation>
+    </citations>
+</tool>