diff lasttrain.xml @ 0:9a7e91fc6562 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lasttrain.xml	Wed Jun 17 14:50:21 2020 -0400
@@ -0,0 +1,121 @@
+<tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy0" profile="18.01">
+
+    <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description>
+
+    <macros>
+        <import>macros_last.xml</import>
+    </macros>
+
+    <requirements>
+        <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+        #if $db_opts.db_opts_input == 'lastdb'
+            ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
+        #end if
+
+        last-train
+
+        -Q $init_options.Q
+
+        -r $init_options.r
+        -q $init_options.q
+
+        -a $init_options.cost_opt.a
+        -b $init_options.cost_opt.b
+        -A $init_options.cost_opt.A
+        -B $init_options.cost_opt.B
+
+        -D $last_train_opt.align_opt.D
+        -E $last_train_opt.align_opt.E
+        -s $last_train_opt.align_opt.s
+        -S $last_train_opt.align_opt.S
+        -T $last_train_opt.align_opt.T
+        -m $last_train_opt.align_opt.m
+        -k $last_train_opt.align_opt.k
+        -X $last_train_opt.align_opt.X
+
+        -P \${GALAXY_SLOTS:-1}
+
+        #if $db_opts.db_opts_input == 'db'
+            '${"' '".join(str($db_opts.database.fields.path).split(","))}'
+        #else if $db_opts.db_opts_input == 'lastdb'
+            'db_files/lastdb'
+        #end if
+
+        '$query_fasta'
+
+        >'$outfile'
+
+    ]]></command>
+
+    <inputs>
+        <expand macro="input_db" />
+        <param name="query_fasta" type="data" format="FASTA" label="Queries input files" />
+        <conditional name="init_options">            
+            <param argument="-Q" type="select" multiple="false" label="Input format">
+                <option value="0" selected="true">Fasta or fastq-ignore</option>
+                <option value="1">Fastq-sanger</option>
+            </param>
+            <when value="0">
+                <param argument="-r" type="integer" value="5" label="Match score"/>
+                <param argument="-q" type="integer" value="5" label="Mismatch cost"/>
+                <expand macro="cost_macro" a="15" b="3"/>
+            </when>
+            <when value="1">
+                <param argument="-r" type="integer" value="6" label="Match score"/>
+                <param argument="-q" type="integer" value="18" label="Mismatch cost"/>
+                <expand macro="cost_macro" a="21" b="9"/>
+            </when>
+        </conditional>
+
+        <section name="last_train_opt" title="Last-train options" expanded="false">
+            <!-- Training options missing  -->
+            <section name="align_opt" title="Alignment options" expanded="true">
+                <param argument="-D" type="integer" value="1000000" label="Query letters per random alignment"/>
+                <param argument="-E" type="integer" value="10" label="Maximum expected alignments per square giga"/>
+                <param argument="-s" type="select" multiple="false" label="Query strand to use">
+                    <option value="0">Reverse</option>
+                    <option value="1" selected="true">Forward</option>
+                    <option value="2">Both</option>
+                </param>
+                <param argument="-S" type="select" multiple="false" label="Score matrix applies to forward strand of:">
+                    <option value="0">Reference</option>
+                    <option value="1" selected="true">Query</option>
+                </param>                
+                <!--<param name="gapless_align" argument="-C" type="integer" value="" label="Omit gapless alignments in COUNT others with > score-per-length"/>-->
+                <param argument="-T" type="select" multiple="false" label="Type of alignment:">
+                    <option value="0" selected="true">Local</option>
+                    <option value="1">Overlap</option>
+                </param>
+                <param argument="-m" type="integer" value="10" label="Maximum initial matches per query position"/>
+                <param argument="-k" type="integer" value="1" label="Use initial matches starting at every STEP-th position in each query"/>
+                <param argument="-X" type="select" multiple="false" label="N/X is ambiguous in:">
+                    <option value="0" selected="true">Neither sequence</option>
+                    <option value="1">Reference</option>
+                    <option value="2">Query</option>
+                    <option value="3">Both</option>
+                </param>
+            </section>
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="outfile" format="txt" label="LAST train from ${on_string}" />
+    </outputs>
+
+    <tests>
+        <test>
+            <conditional name="db_opts">
+                <param name="db_opts_input" value="db"/>
+                <param name="database" value="humdb"/>
+            </conditional>
+            <param name="query_fasta" value="fuguMito.fa"/>
+            <output name="outfile" file="last_train.txt" ftype="txt" lines_diff="22"/>
+        </test>
+    </tests>
+
+    <help>@LAST_HELP@</help>
+    <citations><expand macro="citations"/></citations>
+</tool>