--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gffcompare.xml	Sat May 22 07:35:00 2021 +0000
@@ -0,0 +1,173 @@
+<tool id="gffcompare" name="GffCompare">
+    <description>compare assembled transcripts to a reference annotation</description>
+    <requirements>
+        <container type="docker">bianca7/lncrna:gffcompare</container>
+    </requirements>
+    <!--version_command>gffcompare -v | awk '{print $2}'</version_command-->
+    <command detect_errors="aggressive"><![CDATA[
+#import re
+
+#set escaped_element_identifiers = [re.sub('[^\w\-]', '_', str(_.element_identifier)) for _ in $gffinputs]
+#for $input, $escaped_element_identifier in zip($gffinputs, $escaped_element_identifiers):
+    ln -s '$input' '$escaped_element_identifier' &&
+#end for
+#if $seq_data.use_seq_data == "Yes":
+    #if $seq_data.seq_source.index_source == "history":
+        ln -s '$seq_data.seq_source.ref_file' ref_seq.fa &&
+    #else:
+        ln -s '${seq_data.seq_source.index.fields.path}' ref_seq.fa &&
+    #end if
+#end if
+
+#if $annotation.use_ref_annotation == "Yes":
+    #if $annotation.ref_source.ref_source_sel == "history":
+        ln -s '$annotation.ref_source.reference_annotation' ref_annotation &&
+    #else
+        ln -s '$annotation.ref_source.index.fields.path' ref_annotation &&
+    #end if
+#end if
+
+gffcompare
+## Use annotation reference?
+#if $annotation.use_ref_annotation == "Yes":
+    -r ref_annotation
+    $annotation.ignore_nonoverlapping_reference
+    $annotation.ignore_nonoverlapping_transfrags
+    $annotation.strict_match
+#end if
+#if $annotation.refmap_tmap == "":
+    -T
+#end if
+
+## Use sequence data?
+#if $seq_data.use_seq_data == "Yes":
+    -s ref_seq.fa
+#end if
+
+$discard_single_exon
+$discard_duplicates
+$no_merge
+-e $max_dist_exon
+-d $max_dist_group
+$chr_stats
+-p '$adv_output.p'
+$adv_output.A
+$adv_output.C
+$adv_output.X
+$adv_output.K
+
+#for $escaped_element_identifier in $escaped_element_identifiers:
+    '$escaped_element_identifier'
+#end for
+
+    ]]></command>
+    <inputs>
+        <param format="gtf" name="gffinputs" type="data" label="GTF inputs for comparison" help="" multiple="true" />
+        <conditional name="annotation">
+            <param label="Use Reference Annotation" name="use_ref_annotation" type="select">
+                <option value="No">No</option>
+                <option value="Yes">Yes</option>
+            </param>
+            <when value="Yes">
+                <conditional name="ref_source">
+                    <param label="Choose the source for the reference annotation" name="ref_source_sel" type="select">
+                        <option value="cached">Locally cached</option>
+                        <option value="history">History</option>
+                    </param>
+                    <when value="cached">
+                        <param argument="-r" label="Using reference annotation" name="index" type="select">
+                            <options from_data_table="gene_sets">
+                                <!--filter column="dbkey" key="dbkey" ref="gffinputs" type="data_meta" /-->
+                            </options>
+                            <validator message="No reference annotation is available for the build associated with the selected input dataset" type="no_options" />
+                        </param>
+                    </when>
+                    <when value="history">
+                        <param argument="-r" format="gff3,gtf" help="Requires an annotation file in GFF3 or GTF format." label="Reference Annotation" name="reference_annotation" type="data" />
+                    </when>
+                </conditional>
+                <param argument="-R" falsevalue="" help="consider only the reference transcripts that overlap any of the input transfrags (Sn correction)" label="Ignore reference transcripts that are not overlapped by any input transfrags" name="ignore_nonoverlapping_reference" truevalue="-R" type="boolean" />
+                <param argument="-Q" falsevalue="" help="consider only the input transcripts that overlap any of the reference transcripts (Sp correction). Warning: this will discard all 'novel' loci!" label="Ignore input transcripts that are not overlapped by any reference transcripts" name="ignore_nonoverlapping_transfrags" truevalue="-Q" type="boolean" />
+                <param argument="--strict-match" name="strict_match" type="boolean" checked="false" truevalue="--strict-match" falsevalue=""  label="the match code '=' is only assigned when all exon boundaries match" help="code '~' is assigned for intron chain match or single-exon" />
+                <param argument="-T" name="refmap_tmap" label="Generate tmap or refmap file for each input file" type="select" multiple="True">
+                    <option value="refmap" selected="True">refmap</option>
+                    <option value="tmap" selected="True">tmap</option>
+                </param>
+            </when>
+            <when value="No">
+                <param argument="-T" name="refmap_tmap" label="Generate tmap file for each input file" type="select" multiple="True">
+                    <option value="tmap" selected="True">tmap</option>
+                </param>
+            </when>
+        </conditional>
+        <conditional name="seq_data">
+            <param help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff." label="Use Sequence Data" name="use_seq_data" type="select">
+                <option value="No">No</option>
+                <option value="Yes">Yes</option>
+            </param>
+            <when value="No"/>
+            <when value="Yes">
+                <conditional name="seq_source">
+                    <param label="Choose the source for the reference sequence" name="index_source" type="select">
+                        <option value="cached">Locally cached</option>
+                        <option value="history">History</option>
+                    </param>
+                    <when value="cached">
+                        <param argument="-s" label="Using reference genome" name="index" type="select">
+                            <options from_data_table="fasta_indexes">
+                                <filter column="dbkey" key="dbkey" ref="gffinputs" type="data_meta" />
+                            </options>
+                            <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
+                        </param>
+                    </when>
+                    <when value="history">
+                        <param argument="-s" format="fasta" label="Using reference file" name="ref_file" type="data" />
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+        <param name="discard_single_exon" argument="-M/-N" type="select" label="Discard single-exon transcripts" help="If -S and also --strict-match is given, exact matching of all exon boundaries is required">
+            <option selected="True" value="">No</option>
+            <option value="-M">Discard single-exon transfrags and reference transcripts</option>
+            <option value="-N">Discard single-exon reference transcripts</option>
+        </param>
+        <param label="Discard duplicates" name="discard_duplicates" type="select">
+            <option value="">None</option>
+            <option value="-D">discard 'duplicate' query transfrags within a single sample (-D)</option>
+            <option value="-S">Only discard 'duplicate' query or reference transcripts if their boundaries are fully contained within other, larger or identical transfrags (-S)</option>
+        </param>
+        <param name="no_merge" argument="--no-merge" type="boolean" checked="false" truevalue="--no-merge" falsevalue=""  label="Disable close-exon merging" help="Default: merge exons separated by 'introns' shorter than 5 bases" />
+        <param argument="-e" help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" label="Max. Distance for assessing exon accuracy" name="max_dist_exon" type="integer" value="100" />
+        <param argument="-d" help="max. distance (range) for grouping transcript start sites. Default: 100" label="Max distance for transcript grouping" name="max_dist_group" type="integer" value="100" />
+        <param name="chr_stats" argument="--chr-stats" type="boolean" checked="false" truevalue="--chr-stats" falsevalue="" label="Show summary and accuracy data separately for each reference sequence in the transcript accuracy data set" />
+        <section name="adv_output" title="Options for the combined GTF output file">
+            <param argument="-p"  type="text" value="TCONS" label="name prefix for consensus transcripts" help="for combined.gtf" />
+            <param argument="-C"  type="boolean" checked="false" truevalue="-C" falsevalue=""  label="discard matching and 'contained' transfrags" help="i.e. collapse intron-redundant transfrags across all query files" />
+            <param argument="-A"  type="boolean" checked="false" truevalue="-A" falsevalue=""  label="discard the 'contained' transfrags except intron-redundant transfrags starting with a different 5' exon" help="like -C but does not discard intron-redundant transfrags if they start with a different 5' exon" />
+            <param argument="-X"  type="boolean" checked="false" truevalue="-X" falsevalue=""  label="discard the 'contained' transfrags also if ends stick out within the container's introns" help="like -C but also discard contained transfrags if transfrag ends stick out within the container's introns" />
+            <param argument="-K"  type="boolean" checked="false" truevalue="-K" falsevalue=""  label="do NOT discard any redundant transfrag matching a reference" help="for -C/-A/-X" />
+        </section>
+    </inputs>
+    <outputs>
+        <data format="txt" from_work_dir="gffcmp.stats" label="${tool.name} on ${on_string}: transcript accuracy" name="transcripts_stats" />
+        <data format="tabular" from_work_dir="gffcmp.loci" label="${tool.name} on ${on_string}: loci" name="transcripts_loci" />
+        <data format="tabular" from_work_dir="gffcmp.tracking" label="${tool.name} on ${on_string}: data ${gffinputs[0].hid} tracking file" name="transcripts_tracking" />
+        <data format="gtf" from_work_dir="gffcmp.combined.gtf" label="${tool.name} on ${on_string}: combined transcripts" name="transcripts_combined">
+            <filter>(isinstance(gffinputs, list) and len(gffinputs) > 1) or annotation['use_ref_annotation'] == "No"</filter>
+        </data>
+        <data format="gtf" from_work_dir="gffcmp.annotated.gtf" label="${tool.name} on ${on_string}: annotated transcripts" name="transcripts_annotated">
+            <filter>not (isinstance(gffinputs, list) and len(gffinputs) > 1) and annotation['use_ref_annotation'] == "Yes"</filter>
+        </data>
+        <collection name="refmap_output" type="list" label="${tool.name} on ${on_string}: refmap">
+            <discover_datasets pattern="gffcmp\.(?P&lt;designation&gt;.+)\.refmap" ext="tabular" />
+            <filter>annotation['refmap_tmap'] != None and 'refmap' in annotation['refmap_tmap']</filter>
+        </collection>
+        <collection name="tmap_output" type="list" label="${tool.name} on ${on_string}: tmap">
+            <discover_datasets pattern="gffcmp\.(?P&lt;designation&gt;.+)\.tmap" ext="tabular" />
+            <filter>annotation['refmap_tmap'] != None and 'tmap' in annotation['refmap_tmap']</filter>
+        </collection>
+    </outputs>
+    <citations>
+        <citation type="doi">10.1038/nbt.1621</citation>
+    </citations>
+</tool>