diff tools/seq_filter_by_id/seq_filter_by_id.xml @ 3:44ab4c0f7683 draft

Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/seq_filter_by_id/seq_filter_by_id.xml	Fri Oct 11 04:37:12 2013 -0400
@@ -0,0 +1,125 @@
+<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.0.6">
+    <description>from a tabular file</description>
+    <requirements>
+        <requirement type="package" version="1.62">biopython</requirement>
+        <requirement type="python-module">Bio</requirement>
+    </requirements>
+    <version_command interpreter="python">seq_filter_by_id.py --version</version_command>
+    <command interpreter="python">
+seq_filter_by_id.py "$input_file" "$input_file.ext"
+#if $output_choice_cond.output_choice=="both"
+ $output_pos $output_neg
+#elif $output_choice_cond.output_choice=="pos"
+ $output_pos -
+#elif $output_choice_cond.output_choice=="neg"
+ - $output_neg
+#end if
+## TODO - Decide on best way to expose multiple ID files via the XML wrapper.
+## Single tabular file, can call the Python script with either UNION or INTERSECTION
+UNION "$input_tabular" "$columns"
+    </command>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <inputs>
+        <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to filter on the identifiers" help="FASTA, FASTQ, or SFF format." />
+        <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
+        <param name="columns" type="data_column" data_ref="input_tabular" multiple="True" numerical="False" label="Column(s) containing sequence identifiers" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
+            <validator type="no_options" message="Pick at least one column"/>
+        </param>
+        <conditional name="output_choice_cond">
+            <param name="output_choice" type="select" label="Output positive matches, negative matches, or both?">
+                <option value="both">Both positive matches (ID on list) and negative matches (ID not on list), as two files</option>
+                <option value="pos">Just positive matches (ID on list), as a single file</option>
+                <option value="neg">Just negative matches (ID not on list), as a single file</option>
+            </param>
+            <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml -->
+            <when value="both" />
+            <when value="pos" />
+            <when value="neg" />
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output_pos" format="fasta" label="With matched ID">
+            <!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
+            <change_format>
+                <when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
+                <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
+                <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
+                <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
+                <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
+                <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
+            </change_format>
+            <filter>output_choice_cond["output_choice"] != "neg"</filter>
+        </data>
+        <data name="output_neg" format="fasta" label="Without matched ID">
+            <!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
+            <change_format>
+                <when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
+                <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
+                <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
+                <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
+                <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
+                <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
+            </change_format>
+            <filter>output_choice_cond["output_choice"] != "pos"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" />
+            <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" />
+            <param name="columns" value="1" />
+            <param name="output_choice" value="pos" />
+            <output name="output_pos" file="k12_hypothetical.fasta" ftype="fasta" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+By default it divides a FASTA, FASTQ or Standard Flowgram Format (SFF) file in
+two, those sequences with or without an ID present in the tabular file column(s)
+specified. You can opt to have a single output file of just the matching records,
+or just the non-matching ones.
+
+Note that the order of sequences in the original sequence file is preserved, as
+is any Roche XML Manifest in an SFF file. Also, if any sequences share an
+identifier (which would be very unusual in SFF files), duplicates are not removed.
+
+**Example Usage**
+
+You may have performed some kind of contamination search, for example running
+BLASTN against a database of cloning vectors or bacteria, giving you a tabular
+file containing read identifiers. You could use this tool to extract only the
+reads without BLAST matches (i.e. those which do not match your contaminant
+database).
+
+You may have a file of FASTA sequences which has been used with some analysis
+tool giving tabular output, which has then been filtered on some criteria.
+You can then use this tool to divide the original FASTA file into those entries
+matching or not matching your criteria (those with or without their identifier
+in the filtered tabular file).
+
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+This tool uses Biopython to read and write SFF files, so you may also wish to
+cite the Biopython application note (and Galaxy too of course):
+
+Cock et al (2009). Biopython: freely available Python tools for computational
+molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
+http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
+
+This tool is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
+    </help>
+</tool>