diff mergegffs.xml @ 0:2b2efd0c4df8 draft

planemo upload commit 7bc2a91afe5fcf29893e582382aa874eacb1c1ca

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mergegffs.xml	Fri Apr 07 17:27:31 2017 -0400
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+<tool id="mergegff" name="Merge gff using gffutils" version="1.0">
+    <requirements>
+        <requirement type="package" version="0.8">python_2_7_gffutils</requirement>
+	 <requirement type="package" version="1.0">genomegtftools</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <version_command>
+        <![CDATA[
+            MergeGFF version 1.0
+        ]]>
+    </version_command>
+    <command><![CDATA[
+
+
+python $__tool_directory__/mergegffs.py  -p $gff -d $sqlitedb -o $output
+#if $blastp:
+    -b '$blastp'
+#end if
+#if $blastx:
+    -x '$blastx'
+#end if
+#if $hmmscan:
+    -f '$hmmscan'
+#end if
+#if $tmhmm:
+    -t '$tmhmm'
+#end if
+#if $signalp:
+    -s '$signalp'
+#end if
+
+
+    ]]></command>
+    <inputs>
+         <!--
+        <param name="transcriptome" type="data" format="fasta" optional="false" label="Transcripts" help="Assembled Transcripts fasta" />
+        <param name="peptides" type="data" format="fasta" optional="false" label="Peptide predictions" help="Predicted peptides in fasta format" />
+        <param name="gene_trans_map" type="data" format="tabular" optional="false" label="Genes to transcripts map" help="Genes to transcripts map output. Containing correspondance between gene ids and transcript ids either generated by Trinity of generated with a clustering algorithm " />
+      -->
+        <param name="gff" type="data" format="gff" optional="false" label="Peptides coordinates" help="Peptides prediction coordinates in gff format " />
+
+        <param name="blastp" type="data" format="tabular" optional="true" label="BLASTP: Peptides vs related species" help="[optional] NCBI BLAST+ blastp output. Output format: XML" />
+        <param name="blastx" type="data" format="tabular" optional="true" label="BLASTX: Transcripts vs related species" help="[optional] NCBI BLAST+ blastx output. Output format: XML" />
+        <param name="hmmscan" type="data" format="txt" optional="true" label="HMMER hmmscan: Peptides vs PFAM" help="[optional] HMMER hmmscan output: Table of per-domain hits. Output format: Table of per-domain hits (--domtblout)" />
+        <param name="tmhmm" type="data" format="tabular" optional="true" label="TMHMM on Peptides" help="[optional]"/>
+        <param name="signalp" type="data" format="tabular" optional="true" label="SignalP on Peptides" help="[optional]" />
+
+        <conditional name="cond_modify">
+            <param name="select_existing" type="select" label="Use an existing gffutils db from history">
+                <option value="yes" selected="True">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes">
+                <param name="gffutils_sqlite_in" type="data" format="sqlite" optional="false" label="Existing GFFUtils SQLite database" help="http://daler.github.io/gffutils/index.html" />
+            </when>
+            <when value="no" />
+        </conditional>
+
+        <section name="filter_option" title="Filter options" expanded="False">
+            <param argument="-E" type="float" value="1e-5" label="Maximum E-value for reporting best blast hit and associated annotations." />
+
+        </section>
+        <param name="keep_sqlite" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep the sqlite database file" help="Can be used for visualization purpose" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="Merged gff" >
+        </data>
+        <data name="sqlitedb" format="sqlite" from_work_dir="Trinotate.sqlite" label="Trinotate sqlite database" >
+            <filter>keep_sqlite</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="gff" ftype="gff" value="Trinity.fasta.transdecoder.gff3" />
+            <param name="blastp" ftype="tabular" value="swissprot.blastp.outfmt6" />
+            <param name="blastx" ftype="tabular" value="swissprot.blastx.outfmt6" />
+            <param name="hmmscan" ftype="txt" value="TrinotatePFAM.out" />
+            <param name="tmhmm" ftype="tabular" value="tmhmm.out" />
+            <param name="signalp" ftype="tabular" value="signalp.out" />
+            <param name="keep_sqlite" value="false" />
+            <output name="output" ftype="tabular" file="output.gff" />
+        </test>
+
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+This tool loads annotations from multiple tools into a gffutils sqlite database and outputs a single gff file containing all annotations.
+The sqlite db can be used for filtering and visualization.
+
+Based on https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate
+
+
+--------
+
+**Suggested upstream Galaxy tools**
+
+Transcripts
+
+ - Trinity: iuc/trinity_
+
+.. _trinity: https://toolshed.g2.bx.psu.edu/repository?repository_id=faf6028922d9220a
+
+Peptides
+
+ - TransDecoder: iuc/transdecoder_
+
+.. _transdecoder: https://toolshed.g2.bx.psu.edu/repository?repository_id=7a2a8151a50f8099
+
+Genes to transcripts map
+
+ - Generate gene to transcript map for Trinity assembly: iuc/trinity_gene_to_trans_map_
+
+.. _trinity_gene_to_trans_map: https://toolshed.g2.bx.psu.edu/repository?repository_id=faf6028922d9220a
+
+BLASTP: Peptides vs Uniprot.SwissProt
+
+ - NCBI BLAST+ blastp: devteam/ncbi_blast_plus_
+
+.. _ncbi_blast_plus: https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c
+
+BLASTX: Transcripts vs Uniprot.SwissProt
+
+ - NCBI BLAST+ blastx: devteam/ncbi_blast_plus_
+
+.. _ncbi_blast_plus: https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c
+
+HMMER hmmscan: Peptides vs PFAM
+
+ - HMMER hmmscan: iuc/hmmer_hmmscan_
+
+.. _hmmer_hmmscan: https://toolshed.g2.bx.psu.edu/repository?repository_id=a2cc4683090b1800
+
+TMHMM on Peptides
+
+ - TMHMM 2.0: peterjc/tmhmm_and_signalp_
+
+.. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a
+
+SignalP on Peptides
+
+ - SignalP 3.0: peterjc/tmhmm_and_signalp_
+
+.. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a
+
+
+
+
+--------
+
+
+    ]]></help>
+    <citations>
+
+    </citations>
+</tool>