--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/align_and_estimate_abundance.xml	Mon Aug 01 14:43:15 2016 -0400
@@ -0,0 +1,309 @@
+<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.0">
+    <description>on a de novo assembly of RNA-Seq data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="1.1.2">bowtie</requirement>
+        <requirement type="package" version="2.2.6">bowtie2</requirement>
+        <requirement type="package" version="1.2">samtools</requirement>
+        <requirement type="package" version="1.2.28">rsem</requirement>
+        <requirement type="package" version="1.5.1">eXpress</requirement>
+        <requirement type="package" version="0.6.0">salmon</requirement>
+    </expand>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+        ln -s '$transcripts' input.fa &&
+
+        #if $inputs.paired_or_single == "paired":
+            #if $inputs.left_input.is_of_type('fasta'):
+                ln -s '$inputs.left_input' paired_left.fa &&
+                ln -s '$inputs.right_input' paired_right.fa
+            #else:
+                ln -s '$inputs.left_input' paired_left.fq &&
+                ln -s '$inputs.right_input' paired_right.fq
+            #end if
+        #else:
+            #if $inputs.left_input.is_of_type('fasta'):
+                ln -s '$inputs.input' single.fa
+            #else:
+                ln -s '$inputs.input' single.fq
+            #end if
+        #end if
+
+        &&
+
+        align_and_estimate_abundance.pl
+
+        --transcripts input.fa
+
+        --est_method $method.est_method
+        #if $method.est_method == "RSEM" or $method.est_method == "eXpress":
+            --aln_method $method.aln_method
+        #else if $method.est_method == "salmon":
+            --salmon_idx_type $method.salmon_idx_type
+        #end if
+
+        #if $inputs.paired_or_single == "paired":
+
+            #if $inputs.left_input.is_of_type('fasta'):
+                --left paired_left.fa --right paired_right.fa --seqType fa
+            #else:
+                --left paired_left.fq --right paired_right.fq --seqType fq
+            #end if
+
+            #if $inputs.strand.is_strand_specific:
+                --SS_lib_type $inputs.strand.library_type
+            #end if
+
+            --max_ins_size $inputs.paired_fragment_length
+
+        #else:
+            #if $inputs.input.is_of_type('fasta'):
+                --single single.fa --seqType fa
+            #else:
+                --single single.fq --seqType fq
+            #end if
+
+            #if $inputs.strand.is_strand_specific:
+                --SS_lib_type $inputs.strand.library_type
+            #end if
+        #end if
+
+        ## Additional parameters.
+        #if $additional_params.gene_map.has_gene_map == "no":
+            --gene_trans_map $additional_params.gene_map.gene_trans_map
+        #else
+            --trinity_mode
+        #end if
+
+        --prep_reference
+
+        --output_dir output
+
+        ## CPU
+        --thread_count \${GALAXY_SLOTS:-4}
+    ]]></command>
+    <inputs>
+        <param format="fasta" name="transcripts" argument="--transcripts" type="data" label="Transcripts" help="de novo assembly of RNA-Seq data"/>
+        <conditional name="inputs">
+            <param name="paired_or_single" type="select" label="Paired or Single-end data?">
+                <option value="paired">Paired</option>
+                <option value="single">Single</option>
+            </param>
+            <when value="paired">
+                <param format="fasta,fastqsanger" name="left_input" argument="--left" type="data" label="Left/Forward strand reads" help=""/>
+                <param format="fasta,fastqsanger" name="right_input" argument="--right" type="data" label="Right/Reverse strand reads" help=""/>
+                <conditional name="strand">
+                    <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
+                    <when value="false">
+                    </when>
+                    <when value="true">
+                        <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
+                            <option value="FR">Forward-Reverse</option>
+                            <option value="RF">Reverse-Forward</option>
+                        </param>
+                    </when>
+                </conditional>
+                <param name="paired_fragment_length" argument="--max_ins_size" type="integer" value="800" min="1" label="Maximum insert size" help="bowtie -X parameter"/>
+            </when>
+            <when value="single">
+                <param format="fasta,fastqsanger" argument="--single" name="input" type="data" label="Single-end reads" help=""/>
+                <conditional name="strand">
+                    <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
+                    <when value="false">
+                    </when>
+                    <when value="true">
+                        <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
+                            <option value="F">F</option>
+                            <option value="R">R</option>
+                        </param>
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+
+        <conditional name="method">
+            <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
+                <option value="RSEM">RSEM</option>
+                <option value="eXpress">eXpress</option>
+                <option value="salmon">Salmon</option>
+            </param>
+            <when value="RSEM">
+                <param type="select" name="aln_method" argument="--aln_method" label="Alignment method">
+                    <option value="bowtie">Bowtie</option>
+                    <option value="bowtie2">Bowtie2</option>
+                </param>
+            </when>
+            <when value="eXpress">
+                <param type="select" name="aln_method" argument="--aln_method" label="Alignment method">
+                    <option value="bowtie">Bowtie</option>
+                    <option value="bowtie2">Bowtie2</option>
+                </param>
+            </when>
+            <when value="salmon">
+                <param type="select" name="salmon_idx_type" argument="--salmon_idx_type" label="Index type">
+                    <option value="quasi">Quasi</option>
+                    <option value="fmd">FMD</option>
+                </param>
+            </when>
+        </conditional>
+
+        <section name="additional_params" title="Additional Options" expanded="False">
+            <conditional name="gene_map">
+                <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed">
+                    <option value="yes">Yes</option>
+                    <option value="no">No</option>
+                </param>
+                <when value="yes">
+                </when>
+                <when value="no">
+                    <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" />
+                </when>
+            </conditional>
+
+        </section>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="isoforms_counts_rsem" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/RSEM.isoforms.results">
+            <filter>method['est_method'] == "RSEM"</filter>
+        </data>
+        <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/RSEM.genes.results">
+            <filter>method['est_method'] == "RSEM"</filter>
+        </data>
+
+        <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/results.xprs">
+            <filter>method['est_method'] == "eXpress"</filter>
+        </data>
+        <data format="tabular" name="genes_counts_express" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/results.xprs.genes">
+            <filter>method['est_method'] == "eXpress"</filter>
+        </data>
+
+        <data format="tabular" name="isoforms_counts_salmon" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/quant.sf">
+            <filter>method['est_method'] == "salmon"</filter>
+        </data>
+        <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/quant.sf.genes">
+            <filter>method['est_method'] == "salmon"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="paired_or_single" value="paired"/>
+            <param name="left_input" value="reads.left.fq"/>
+            <param name="right_input" value="reads.right.fq"/>
+            <param name="transcripts" value="raw/Trinity.fasta"/>
+            <param name="library_type" value="RF"/>
+            <param name="est_method" value="RSEM"/>
+            <param name="aln_method" value="bowtie"/>
+            <param name="has_gene_map" value="yes"/>
+            <output name="isoforms_counts_rsem">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
+                    <has_n_columns n="8" />
+                </assert_contents>
+            </output>
+            <output name="genes_counts_rsem">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN0_c0_g1&#009;.*" />
+                    <has_n_columns n="7" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="paired_or_single" value="paired"/>
+            <param name="left_input" value="reads.left.fq"/>
+            <param name="right_input" value="reads.right.fq"/>
+            <param name="transcripts" value="raw/Trinity.fasta"/>
+            <param name="library_type" value="RF"/>
+            <param name="est_method" value="RSEM"/>
+            <param name="aln_method" value="bowtie2"/>
+            <param name="has_gene_map" value="yes"/>
+            <output name="isoforms_counts_rsem">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
+                    <has_n_columns n="8" />
+                </assert_contents>
+            </output>
+            <output name="genes_counts_rsem">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN0_c0_g1&#009;.*" />
+                    <has_n_columns n="7" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="paired_or_single" value="paired"/>
+            <param name="left_input" value="reads.left.fq"/>
+            <param name="right_input" value="reads.right.fq"/>
+            <param name="transcripts" value="raw/Trinity.fasta"/>
+            <param name="library_type" value="RF"/>
+            <param name="est_method" value="eXpress"/>
+            <param name="aln_method" value="bowtie"/>
+            <param name="has_gene_map" value="yes"/>
+            <output name="isoforms_counts_express">
+                <assert_contents>
+                    <has_line_matching expression=".*&#009;TRINITY_DN2_c3_g1_i1&#009;.*" />
+                    <has_n_columns n="15" />
+                </assert_contents>
+            </output>
+            <output name="genes_counts_express">
+                <assert_contents>
+                    <has_line_matching expression="NA&#009;TRINITY_DN3_c0_g1.*" />
+                    <has_n_columns n="15" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="paired_or_single" value="paired"/>
+            <param name="left_input" value="reads.left.fq"/>
+            <param name="right_input" value="reads.right.fq"/>
+            <param name="transcripts" value="raw/Trinity.fasta"/>
+            <param name="library_type" value="RF"/>
+            <param name="est_method" value="salmon"/>
+            <param name="aln_method" value="bowtie"/>
+            <param name="has_gene_map" value="yes"/>
+            <output name="isoforms_counts_salmon">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN2_c3_g1_i1&#009;.*" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+            <output name="genes_counts_salmon">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1.*" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+This tool estimates the abundance of isoforms and genes of a transcriptome assembled with Trinity, using FastQ of a specific sample.
+
+**Inputs**
+
+It takes as input a transcriptome assembled with Trinity and the reads from a RNASeq sample.
+You have to choose between several counting methods.
+
+If you dont align on a Trinity assembly, you need to provide a file of the following (tabular) format to map gene ids to transcript ids:
+
+=========== ================
+gene1       transcript1
+----------- ----------------
+gene2       transcript2
+=========== ================
+
+**Output**
+
+This tool will produce 2 tabular files, with counts for isoforms and genes respectively. More details on this page:
+
+.. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification
+
+
+.. _Trinity: http://trinityrnaseq.github.io
+]]>
+    </help>
+
+    <expand macro="citation" />
+</tool>