diff create.xml @ 16:ba9d0fc8657f draft

Uploaded 20190118

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create.xml	Fri Jan 18 10:12:19 2019 -0500
@@ -0,0 +1,104 @@
+<?xml version="1.0"?>
+<tool name="BloomTree Manager - Create" id="btman_create" version="1.0.0">
+    <description>a Sequence Bloom Tree</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+<![CDATA[
+    python '$__tool_directory__/create.py'
+    
+    --explist '${explist}'
+
+    --qualitycontrol ${conditional_quality.quality_control}
+    #if $conditional_quality.quality_control == '0':
+        --qualitythreshold 0.0
+    #elif $conditional_quality.quality_control == '1':
+        --qualitythreshold ${conditional_quality.quality_threshold}
+    #end if
+
+    --klen ${kmer_len}
+    --minabundance ${min_abundance}
+
+    --outfile '${outfile}'
+]]>
+    </command>
+    <inputs>
+        <param format="tabular" name="explist" type="data" label="Select a file with the list of experiments" help="This should be a tabular file with two columns. Take a look at the tool documentation for a detailed explanation about the its content." />
+
+        <conditional name="conditional_quality">
+            <param name="quality_control" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Apply a quality control procedure" />
+            <when value="1">
+                <param name="quality_threshold" size="1" type="float" value="0.8" min="0.0" max="1.0" label="Quality threshold" help="If the number of sequences flagged as poor quality on the total number of sequences in a file is less than this threshold, the sequence file will be excluded." />
+            </when>
+        </conditional>
+
+        <param name="kmer_len" type="integer" value="21" min="0" label="K-mer length" />
+        <param name="min_abundance" type="integer" value="2" min="0" label="Bloom filter minimum abundance" help="This value is the minimum abundance cutoff for the creation of the Bloom filters. It is worth noting that the same minimum abundance is used for each Bloom filter." />
+    </inputs>
+    <outputs>
+        <data format="txt" name="outfile" label="${tool.name} SBT: Result" from_work_dir="btman.create.txt" />
+    </outputs>
+
+    <help><![CDATA[
+This tool is part of the BloomTree Manager Framework that allow to create a Sequence Bloom Tree starting 
+with a set of FASTA or FASTQ files. It allows also to control the quality of the input dataset and 
+exclude the files that do not reach a specified quality level.
+
+-----
+
+**Input file**
+
+The input file for this tool must contain two columns with their values delimited by a tab.
+The first column contains a list of SRA accessions, and the second column contains a unique identifier
+for each set of SRA accessions.
+
+The input file is structured like the example below::
+    
+    SRR805782  blood
+    SRR837459  blood
+    SRR837458  blood
+    SRR837453  blood
+    SRR837456  blood
+    ...
+    SRR791048  breast
+    SRR553483  breast
+    SRR553482  breast
+    SRR791045  breast
+    ...
+    SRR950876  brain
+    SRR786621  brain
+
+It is worth noting that for each cluster of accessions, every accession should be unique.
+It is indeed possible to repeat an accession in multiple clusters.
+
+The tool will create a Sequence Bloom Tree for each cluster of accessions.
+
+-----
+
+**Output**
+
+The tool returns a single text file only. It contains the a tree identifier, one for
+each cluster of accessions specified in the input file, that can be used with the
+Query tool of the BloomTree Manager Suite to search for the presence of a set of
+specific transcripts.
+
+Take a look at the Query tool documentation for a detailed description about how
+to query a Sequence Bloom Tree.
+
+-----
+
+.. class:: infomark
+
+**Notes**
+
+This Galaxy tool has been developed by Fabio Cumbo.
+
+Please visit this GithHub_repository_ for more information about the BloomTree Manager
+
+.. _GithHub_repository: https://github.com/fabio-cumbo/bloomtree-manager
+    ]]></help>
+
+    <expand macro="citations" />
+</tool>