diff presto_buildconsensus.xml @ 0:7c7df98db5a9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/presto_buildconsensus.xml	Wed May 30 15:37:30 2018 -0400
@@ -0,0 +1,120 @@
+<tool id="presto_buildconsensus" name="pRESTO BuildConsensus" version="@PRESTO_VERSION@">
+    <description>Builds a consensus sequence for each set of input sequences</description>
+    
+    <macros>
+        <import>presto_macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements"/>
+    
+    <version_command>BuildConsensus.py --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$fastq_in' in.fastq &&
+        BuildConsensus.py
+          --nproc "\${GALAXY_SLOTS:-1}"
+          -s in.fastq
+          -n '$n'
+          --bf '$bf'
+          -q '$q'
+          --freq '$freq'
+          #if $maxgap
+            --maxgap '$maxgap'
+          #end if
+          #if $pf
+            --pf '$pf'
+          #end if
+          #if $prcons
+            --prcons '$prcons'
+          #end if
+          #if $cf
+            --cf $cf
+          #end if
+          #if $act
+            --act $act
+          #end if
+          $dep
+          
+          #if $filtering.filter == "diversity"
+            --maxdiv '$filtering.maxdiv'
+          #end if
+          #if $filtering.filter == "error"
+            --maxerror '$filtering.maxerror'
+          #end if
+
+          --outname=tmp 
+          #if $capture_log
+            --log '$log_out'
+          #end if
+    ]]></command>
+
+    <inputs>
+        <param argument="-s" name="fastq_in" type="data" format="fastq" label="Input FASTQ file" help="FASTQ file of sequences with barcodes/UMIs in an annotation."/>
+        <param argument="-n" type="integer" value="1" label="Min Count" help="Minimum number of squences to form a valid consensus."/>
+        <param argument="--bf" type="text" value="BARCODE" label="Barcode Field" help="Name of the annotation field which contains the barcode/UMI sequence."/>
+        <param argument="-q" type="integer" value="0" label="Min Quality" help="Minimum quality under which an ambiguous character is assigned to a consensus base."/>
+        <param argument="--freq" type="float" value="0.6" label="Min Frequency" help="At a given position the fraction of basecalls required to agree to output an unambiguous base."/>
+        <param argument="--maxgap" type="float" value="" optional="true" label="Max Gap Fraction" help="Positions with greater than this fraction of gaps are deleted from the consensus."/>
+        <param argument="--pf" type="text" value="" optional="true" label="Primer Field" help="Name of the annotation field which contains the primer sequence (often PRIMER)."/>
+        <param argument="--prcons" type="float" value="" optional="true" label="Primer Consensus Frequency" help="Specify to define a minimum primer frequency required to assign a consensus primer, and filter out sequences with minority primers from the consensus building step."/>
+        <param argument="--cf" type="text" value="" optional="true" label="Copy Fields"  help="Zero or more space-separated annotations to copy from input sequences to consensus sequences.">
+            <expand macro="text-regex-validator"/>
+        </param>
+        <param argument="--act" type="text" value="" optional="true" label="Copy Actions" help="Space-separated list of actions to take on copied annotations. Must be of same length as Copy Fields. Options are: min,max,sum,set,majority.">
+            <expand macro="text-regex-validator"/>
+        </param>
+        <param argument="--dep" type="boolean" value="false" truevalue="--dep" falsevalue="" label="Dependent Model" help="Specify to calculate consensus quality with a non-independence assumption."/>
+        <expand macro="presto-log-param"/>
+
+        <conditional name="filtering">
+            <param name="filter" type="select" label="Filtering Strategy">
+                <option value="none">No filtering of consensus reads.</option>
+                <option value="diversity">Filter by diversity (average pairwise error rate of input reads).</option>
+                <option value="error">Filters by error rate of input reads vs. consensus.</option>
+            </param>
+            <when value="diversity">
+                <param argument="--maxdiv" type="float" value="" label="Max Diversity" help="Remove consensus reads with average pairwise error between input reads above this cutoff [0-1]."/>
+            </when>
+            <when value="error">
+                <param argument="--maxerror" type="float" value="" label="Max Error" help="Remove consensus reads with average error vs. input reads above this cutoff [0-1]."/>
+            </when>
+            <when value="none"/>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data name="fastq_out" format="fastq" from_work_dir="tmp_consensus-pass.fastq"/>
+        <expand macro="presto-log-output"/>
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="fastq_in" value="presto_buildconsensus_test_input.fastq"/>
+            <param name="n" value="2"/>
+            <param name="pf" value="PRIMER"/>
+            <param name="maxgap" value="0.5"/>
+            <param name="prcons" value="0.6"/>
+            <param name="filter" value="error"/>
+            <param name="maxerror" value="0.1"/>
+            <output name="fastq_out" file="presto_buildconsensus_test_maxerror_output.fastq" sort="true"/>
+        </test>
+        <test>
+            <param name="fastq_in" value="presto_buildconsensus_test_input.fastq"/>
+            <param name="n" value="2"/>
+            <param name="pf" value="PRIMER"/>
+            <param name="maxgap" value="0.5"/>
+            <param name="prcons" value="0.6"/>
+            <param name="filter" value="diversity"/>
+            <param name="maxdiv" value="0.05"/>
+            <output name="fastq_out" file="presto_buildconsensus_test_maxdiv_output.fastq" sort="true"/>
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+Builds a consensus sequence for each set of input sequences.
+
+See the `pRESTO online help <@PRESTO_URL_BASE@/BuildConsensus.html>`_ for more information.
+
+@HELP_NOTE@
+    ]]></help>
+    <expand macro="citations" />
+</tool>