--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flair_collapse.xml	Fri Nov 27 18:45:47 2020 +0000
@@ -0,0 +1,188 @@
+<tool id="flair_collapse" name="FLAIR collapse" version="@TOOL_VERSION@" profile="20.01">
+    <description>defines high-confidence isoforms from flair-corrected reads</description>
+
+    <macros>
+        <import>flair_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+
+    <command detect_errors="exit_code"><![CDATA[
+
+@PREPARE_REF@
+
+ln -s '$input_query' query.bed &&
+
+flair.py collapse
+
+###########
+## Input ##
+###########
+
+-q query.bed
+-r '$input_reads'
+-g reference.fa
+-f '$input_gtf'
+
+#if $input_promotors:
+    -p '$input_promotors'
+#end if
+
+########################
+## Additional Options ##
+########################
+
+-w $additional_options.window
+-s $additional_options.support
+$additional_options.stringent
+
+#if str($additional_options.select_uniqueness):
+    -n str($additional_options.select_uniqueness)
+#end if
+
+$additional_options.isoform
+--max_ends $additional_options.maxends
+$additional_options.trustends
+
+#if str($additional_options.select_filter):
+    -e str($additional_options.select_filter)
+#end if
+
+#########
+## END ##
+#########
+
+    ]]></command>
+    <inputs>
+        <param name="input_query" argument="-q" type="data" format="bed" label="Corrected Reads as BED file"/>
+        <param name="input_reads" argument="-r" type="data" format="fasta,fastq" label="FASTA/FASTQ file of raw reads"/>
+        <expand macro="reference_interface" />
+        <param name="input_gtf" argument="-f" type="data" format="gtf" label="GTF annotation file"/>
+        <param name="input_promotors" optional="true" argument="-p" type="data" format="bed" label="Promotor BED file to identify full-length reads" />
+
+        <!-- Additional Options -->
+        <section name="additional_options" title="Additional Options">
+            <param name="window" argument="-w" type="integer" min="1" value="100" label="Window Size" help="Window size for comparing TSS/TES (Default=100)" />
+            <param name="support" argument="-s" type="integer" min="1" value="3" label="Supporting Reads" help="Minimum number of supporting reads for an isoform (Default=3)" />
+            <param name="stringent" argument="--stringent" type="boolean" checked="false" truevalue="--stringent" falsevalue="" label="Use Stringent Mode" help="Specify if all supporting reads need to be full-length (80% coverage and spanning 25 bp of the first and last exons) (Default=false)"/>
+            <param name="select_uniqueness" argument="-n" type="select" label="Choose the TSS/TES for each unique set of splice junction." >
+                <option value="" selected="true">No Selection</option>
+                <option value="none">Best TSSs/TESs</option>
+                <option value="longest">Single TSS/TES chosen to maximize length</option>
+                <option value="best_only">Single most supported TSS/TES used in conjunction chosen</option>
+            </param>
+            <param name="isoform" argument="-i" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Use Isoform Mode" help="TSS/TES for each isoform will be determined from supporting reads for individual isoforms (Default=false)"/>
+            <param name="maxends" argument="--max_ends" type="integer" min="0" value="2" label="Maximum Number of TSS/TES picked per isoform" help="(Default=2)" />
+            <param name="trustends" argument="--trust_ends" type="boolean" checked="false" truevalue="--trust_ends" falsevalue="" label="Reads are generated from a long read method with minimal fragmentation?" />
+            <param name="select_filter" argument="-e" type="select" label="Filter for isoforms." >
+                <option value="" selected="true">No Filter</option>
+                <option value="nosubset">Any isoforms that are a proper set of another isoform are removed</option>
+                <option value="default">Subset isoforms are removed based on support</option>
+                <option value="comprehensive">Default set + all subset isoforms</option>
+                <option value="ginormous">Comprehensive set + single exon subset isoforms</option>
+            </param>
+            <param name="mapq" argument="--quality" type="integer" min="0" value="1" label="Minimum MAPQ of read assignment to an isoform" help="(Default=1)" />
+        </section>
+
+        <section name="additional_outputs" title="Output Options">
+            <param name="out_format" type="select" multiple="true" optional="true" display="checkboxes" label="Data types">
+                <option value="bed">BED</option>
+                <option value="fasta">FASTA</option>
+            </param>
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="outfile_isoforms_gtf" from_work_dir="flair.collapse.isoforms.gtf" format="gtf" label="${tool.name} on ${on_string}: Isoforms GTF" />
+        <data name="outfile_isoforms_bed" from_work_dir="flair.collapse.isoforms.bed" format="bed" label="${tool.name} on ${on_string}: Isoforms BED">
+            <filter>additional_outputs['out_format'] and 'bed' in additional_outputs['out_format']</filter>
+        </data>
+        <data name="outfile_isoforms_fasta" from_work_dir="flair.collapse.isoforms.fa" format="fasta" label="${tool.name} on ${on_string}: Isoforms FASTA">
+            <filter>additional_outputs['out_format'] and 'fasta' in additional_outputs['out_format']</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="3">
+            <param name="input_query" ftype="bed" value="flair_all_corrected.bed" />
+            <param name="input_reads" ftype="fastq.gz" value="chrM.fastq.gz" />
+            <param name="ref_selector_genome" value="history" />
+            <param name="reffile" ftype="fasta" value="chrM.fa" />
+            <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" />
+            <param name="out_format" value="bed,fasta" />
+            <output name="outfile_isoforms_gtf" ftype="gtf" file="flair.collapse.isoforms.gtf" />
+            <output name="outfile_isoforms_bed" ftype="bed" file="flair.collapse.isoforms.bed" />
+            <output name="outfile_isoforms_fasta" ftype="fasta" file="flair.collapse.isoforms.fa" />
+        </test>
+        <!-- Test with cached genome -->
+        <test expect_num_outputs="3">
+            <param name="input_query" ftype="bed" value="flair_all_corrected.bed" />
+            <param name="input_reads" ftype="fastq.gz" value="chrM.fastq.gz" />
+            <param name="ref_selector_genome" value="cached" />
+            <param name="reffile" value="chrM" />
+            <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" />
+            <param name="out_format" value="bed,fasta" />
+            <output name="outfile_isoforms_gtf" ftype="gtf" file="flair.collapse.isoforms.gtf" />
+            <output name="outfile_isoforms_bed" ftype="bed" file="flair.collapse.isoforms.bed" />
+            <output name="outfile_isoforms_fasta" ftype="fasta" file="flair.collapse.isoforms.fa" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+-------------------
+
+@description@
+
+**flair collapse**
+Defines high-confidence isoforms from corrected reads.
+
+-------------------
+
+**Inputs**
+
+-------------------
+
+(1) Corrected Reads as Bed12 File.
+(2) FASTA/FASTQ file of raw reads. All raw read fastq/fasta files should be concatenated into a single file.
+(3) FASTA of Reference Genome.
+(4) GTF annotation file.
+(5) Promoter regions bed file to identify full-length reads.
+
+-----------
+
+**Outputs**
+
+-----------
+
+Outputs the high-confidence isoforms in several formats:
+(1) bed,
+(2) gtf,
+(3) FASTA.
+
+--------------------
+
+**More Information**
+
+--------------------
+
+See the excellent `FLAIR documentation`_
+
+.. _`FLAIR documentation`: https://github.com/BrooksLabUCSC/flair
+
+
+--------------------
+
+**Galaxy Wrapper Development**
+
+--------------------
+
+@citation@
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>