# HG changeset patch
# User lehmanju
# Date 1592544230 0
# Node ID 14d7fad4a8ab0d47ab97ac15116ba3cc191be50f
# Parent  3ba8f64ada6eb514f3a14228def8c4b63d0d8b58
Uploaded

diff -r 3ba8f64ada6e -r 14d7fad4a8ab rna_quast.xml
--- a/rna_quast.xml	Thu Jun 18 12:21:56 2020 +0000
+++ b/rna_quast.xml	Fri Jun 19 05:23:50 2020 +0000
@@ -1,255 +1,311 @@
 <tool id="rna_quast" name="rnaQUAST" version="2.0.1-0" python_template_version="3.5">
-	<description>A Quality Assessment Tool for De Novo Transcriptome Assemblies</description>
+    <description>A Quality Assessment Tool for De Novo Transcriptome Assemblies</description>
     <requirements>
-	<requirement type="package" version="2.0.1-0">rnaquast</requirement>
+        <requirement type="package" version="2.0.1-0">rnaquast</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+    #for $i in $input
+        ln -s '$i' '$i.element_identifier' &&
+    #end for
+    #if $r
+        #for $rf in $r
+            ln -s '$rf' '$rf.element_identifier' &&
+        #end for
+    #end if
+    #if $gene_coordinates.use_gtf == "true"
+        #for $g in $gene_coordinates.gtf
+            ln -s '$g' '$g.element_identifier' &&
+        #end for
+    #end if
+    mkdir outputdir &&
 
-      	#for $i in $input
-		ln -s '$i' '$i.element_identifier' &&
-	#end for
-	#if $ref.use_ref == "true"	
-		#for $rf in $ref.r
-			ln -s '$rf' '$rf.element_identifier' &&
-		#end for
-	#end if 
-	#if $gene_coordinates.use_gtf == "true"
-		#for $g in $gene_coordinates.gtf
-			ln -s '$g' '$g.element_identifier' &&
-		#end for
-	#end if	
-	mkdir outputdir && rnaQUAST.py 
-	--transcripts
-	#for $i in $input
-		'$i.element_identifier' 	
-	#end for
-	$strand_specific
-	#if $ref.use_ref == "true"
-		-r 
-		#for $rf in $ref.r
-			'$rf.element_identifier' 	
-		#end for
-	#end if
-	#if $gene_coordinates.use_gtf == "true"
-		--gtf 
-		#for $g in $gene_coordinates.gtf
-			'$g.element_identifier' 	
-		#end for
-		$gene_coordinates.disable_infer_genes
-		$gene_coordinates.disable_infer_transcripts
-	#end if
-	$prokaryote
-	--min_alignment '$min_alignment'
-	$no_plots
-	$blat
-	$busco_lineage
-	$gene_mark
-	--lower_threshold $lower_threshold
-	--upper_threshold $upper_threshold
-	
-	-o outputdir 
-	
+    rnaQUAST.py
+    --transcripts
+    #for $i in $input
+        '$i.element_identifier'
+    #end for
+    $strand_specific
+    #if $r
+        -r
+        #for $rf in $r
+            '$rf.element_identifier'
+        #end for
+    #end if
+    #if $gene_coordinates.use_gtf == "true"
+        --gtf
+        #for $g in $gene_coordinates.gtf
+            '$g.element_identifier'
+        #end for
+        $gene_coordinates.disable_infer_genes
+        $gene_coordinates.disable_infer_transcripts
+    #end if
+    $prokaryote
+    --min_alignment '$min_alignment'
+    #if "pdf" not in $out_sr and "plots" not in $out_add
+        --no_plots
+    #end if
+    $blat
+    $busco_lineage
+    $gene_mark
+    --lower_threshold $lower_threshold
+    --upper_threshold $upper_threshold
+    -o outputdir
+
+    && mkdir details 
+    #for $i in $input
+        #set basename = os.path.splitext(str($i.element_identifier))[0]
+        && mv outputdir/'$basename'_output details/'$basename'
+    #end for
+
     ]]></command>
     <inputs>
-	<param name="input" type="data" format="fasta" multiple="true" label="Chromosomes/scaffolds file"/>
-	<param name="strand_specific" argument="-ss" type="boolean" truevalue="-ss" falsevalue="" checked="false" label="Set if transcripts were assembled using strand-specific RNA-Seq data in order to benefit from knowing whether the transcript originated from the + or - strand."/>
-	<param name="r" optional="true" argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" />
-		
-	<conditional name="gene_coordinates">
-		<param name="use_gtf" type="select" label="Use file with gene coordinates in GTF/GFF format (needs information about parent relations)?" help="We recommend to use files downloaded from GENCODE or Ensembl.">
-			<option value="true" selected="true">Yes</option>
-			<option value="false">No</option>
-		</param>
-		<when value="true">
-			<param name="gtf" argument="--gtf" type="data" format="gtf, gff, gff3" multiple="true" label="GTF/GFF file"/>
-			<param name="disable_infer_genes" argument="--disable_infer_genes" type="boolean" truevalue="--disable_infer_genes" falsevalue="" checked="false" label="Use true if your GTF file already contains genes records, otherwise gffutils will fix it. Note that gffutils may work for quite a long time."/>
-			<param name="disable_infer_transcripts" argument="--diable_infer_transcripts" type="boolean" truevalue="--disable_infer_transcripts" falsevalue="" checked="false" label=" True if your GTF file already contains transcripts records, otherwise gffutils will fix it. Note that gffutils may work for quite a long time."/>
-		</when>
-		<when value="false">
-		</when>
-	</conditional>
-	<param name="prokaryote" argument="--prokaryote" type="boolean" truevalue="--prokaryote" falsevalue="" checked="false" label="Is genome prokararyotic?"/>
-	<param name="min_alignment" argument="--min_alignment" type="integer" value="50" label="Minimal alignment length to be used"/>
-	<param name="no_plots" argument="--no_plots" type="boolean" truevalue="" falsevalue="--no_plots" checked="true" label="Want to draw plots?" help="Do not draw plots (makes rnaQUAST run a bit faster)."/>
-	<param name="blat" argument="--blat" type="boolean" truevalue="--blat" falsevalue="" checked="false" label="Run with BLAT alignment tool instead of GMAP?" />
-	<param name="busco_lineage" argument="--busco_lineage" type="boolean" truevalue="--busco_lineage" falsevalue="" checked="false" label="Run BUSCO tool?" help="The BUSCO tool detects core genes in the assembly. Use this option to provide path to the BUSCO lineage data (Eukaryota, Metazoa, Arthropoda, Vertebrata or Fungi)."/>
-	<param name="gene_mark" argument="--gene_mark" type="boolean" truevalue="--gene_mark" falsevalue="" checked="false" label="Run with GeneMarkS-T gene prediction tool?"/>
-	<param name="lower_threshold" argument="--lower_threshold" type="integer" value="50" label="Lower threshold for x_assembled/covered/matched metrics."/>
-	<param name="upper_threshold" argument="--upper_threshold" type="integer" value="95" label="Upper threshold for x_assembled/covered/matched metrics."/>
-	<param name="logs_on" type="boolean" checked="true" label="Want to output the logs?"/>
+        <param name="input" type="data" format="fasta" multiple="true" label="Chromosomes/scaffolds file"/>
+        <param name="strand_specific" argument="-ss" type="boolean" truevalue="-ss" falsevalue="" checked="false" label="Set if transcripts were assembled using strand-specific RNA-Seq data in order to benefit from knowing whether the transcript originated from the + or - strand."/>
+        <param name="r" optional="true" argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" />
+        <conditional name="gene_coordinates">
+            <param name="use_gtf" type="select" label="Use file with gene coordinates in GTF/GFF format (needs information about parent relations)?" help="We recommend to use files downloaded from GENCODE or Ensembl.">
+                <option value="true" selected="true">Yes</option>
+                <option value="false">No</option>
+            </param>
+            <when value="true">
+                <param name="gtf" argument="--gtf" type="data" format="gtf, gff, gff3" multiple="true" label="GTF/GFF file"/>
+                <param name="disable_infer_genes" argument="--disable_infer_genes" type="boolean" truevalue="--disable_infer_genes" falsevalue="" checked="false" label="Use true if your GTF file already contains genes records, otherwise gffutils will fix it. Note that gffutils may work for quite a long time."/>
+                <param name="disable_infer_transcripts" argument="--diable_infer_transcripts" type="boolean" truevalue="--disable_infer_transcripts" falsevalue="" checked="false" label=" True if your GTF file already contains transcripts records, otherwise gffutils will fix it. Note that gffutils may work for quite a long time."/>
+            </when>
+            <when value="false">
+            </when>
+        </conditional>
+        <param name="prokaryote" argument="--prokaryote" type="boolean" truevalue="--prokaryote" falsevalue="" checked="false" label="Is genome prokararyotic?"/>
+        <param name="min_alignment" argument="--min_alignment" type="integer" value="50" label="Minimal alignment length to be used"/>
+        <param name="blat" argument="--blat" type="boolean" truevalue="--blat" falsevalue="" checked="false" label="Run with BLAT alignment tool instead of GMAP?" />
+        <param name="busco_lineage" argument="--busco_lineage" type="boolean" truevalue="--busco_lineage" falsevalue="" checked="false" label="Run BUSCO tool?" help="The BUSCO tool detects core genes in the assembly. Use this option to provide path to the BUSCO lineage data (Eukaryota, Metazoa, Arthropoda, Vertebrata or Fungi)."/>
+        <param name="gene_mark" argument="--gene_mark" type="boolean" truevalue="--gene_mark" falsevalue="" checked="false" label="Run with GeneMarkS-T gene prediction tool?"/>
+        <param name="lower_threshold" argument="--lower_threshold" type="integer" value="50" label="Lower threshold for x_assembled/covered/matched metrics."/>
+        <param name="upper_threshold" argument="--upper_threshold" type="integer" value="95" label="Upper threshold for x_assembled/covered/matched metrics."/>
+        <param name="out_sr" type="select" multiple="true" label="Short report formats">
+            <option value="tsv" selected="true">tabular</option>
+            <option value="txt">txt</option>
+            <option value="tex">tex</option>
+            <option value="pdf" selected="true">pdf</option>
+        </param>
+        <param name="out_add" type="select" multiple="true" label="Additional outputs">
+            <option value="logs">Logs</option>
+            <option value="plots" selected="true">Plots (only for n>1)</option>
+            <option value="comparison" selected="true">Comparison for Chromosomes/scaffolds files (only for n>1)</option>
+            <option value="details" selected="true">Details per Chromosomes/scaffolds file</option>
+        </param>
+
     </inputs>
 
     <outputs>
-	<data name="short_report_pdf" format="pdf" label="${tool.name} on ${on_string}:  PDF report" from_work_dir="outputdir/short_report.pdf">
-		<filter>no_plots</filter>
-	</data>
-	<data name="short_report_txt" format="txt" label="${tool.name} on ${on_string}:  TXT report" from_work_dir="outputdir/short_report.txt"/>
-	<data name="short_report_tex" format="txt" label="${tool.name} on ${on_string}:  TEX report" from_work_dir="outputdir/short_report.tex"/>
-	<data name="short_report_tsv" format="tabular" label="${tool.name} on ${on_string}:  TSV report" from_work_dir="outputdir/short_report.tsv"/>
-
-	<collection name="list_logs" type="list" label="Logs" >
-		<filter> logs_on </filter>
-    		<discover_datasets ext="txt" pattern="(?P&lt;name&gt;.+)\.log"  directory="outputdir/logs/" visible="false" />
-	</collection>
-	<collection name="list_comparison_png" type="list" label="Comparison PNGs" >
-		<filter> len(input)>1 and no_plots </filter>
-    		<discover_datasets ext="png" pattern="(?P&lt;name&gt;.+)\.png"  directory="outputdir/comparison_output/" visible="false" />
-	</collection>
-	<collection name="list_comparison" type="list" label="Comparison Output Texts" >
-		<filter> len(input)>1 </filter>
-    		<discover_datasets ext="txt" pattern="(?P&lt;name&gt;.+)\.txt"  directory="outputdir/comparison_output/" visible="false" />
-	</collection>
-	<collection name="list_comparison_txt_dir" type="list" label="Comparison txt_dir" >
-		<filter> len(input)>1 and no_plots  </filter>
-    		<discover_datasets ext="txt" pattern="(?P&lt;name&gt;.+)\.txt"  directory="outputdir/comparison_output/txt_dir/" visible="false" />
-	</collection>
-	<collection name="data_collection" type="list" label="Txt ${input[0].element_identifier.split('.')[0]}">
-    		<discover_datasets ext="txt" pattern="(?P&lt;name&gt;.+)\.txt"  directory="outputdir/" visible="false"/>
-		<filter> len(input)>1 </filter>
-	</collection>
+        <data name="short_report_pdf" format="pdf" label="${tool.name} on ${on_string}: pdf report" from_work_dir="outputdir/short_report.pdf">
+            <filter>"pdf" in out_sr</filter>
+        </data>
+        <data name="short_report_txt" format="txt" label="${tool.name} on ${on_string}: txt report" from_work_dir="outputdir/short_report.txt">
+            <filter>"txt" in out_sr</filter>
+        </data>
+        <data name="short_report_tex" format="txt" label="${tool.name} on ${on_string}: tex report" from_work_dir="outputdir/short_report.tex">
+            <filter>"tex" in out_sr</filter>
+        </data>
+        <data name="short_report_tsv" format="tabular" label="${tool.name} on ${on_string}: tsv report" from_work_dir="outputdir/short_report.tsv">
+            <filter>"tsv" in out_sr</filter>
+        </data>
+        <collection name="list_logs" type="list" label="${tool.name} on ${on_string}: logs" >
+            <discover_datasets ext="txt" pattern="(?P&lt;name&gt;.+)\.log"  directory="outputdir/logs/" visible="false" />
+            <filter>"logs" in out_add</filter>
+        </collection>
+        <collection name="list_comparison_png" type="list" label="${tool.name} on ${on_string}: plots" >
+            <discover_datasets ext="png" pattern="(?P&lt;name&gt;.+)\.png"  directory="outputdir/comparison_output/" visible="false" />
+            <filter> len(input)>1 and "plots" in out_add </filter>
+        </collection>
+        <collection name="list_comparison" type="list" label="${tool.name} on ${on_string}: comparison" >
+            <discover_datasets ext="txt" pattern="(?P&lt;name&gt;.+)\.txt"  directory="outputdir/comparison_output/" visible="false" />
+            <filter> len(input)>1 and "comparison" in out_add</filter>
+        </collection>
+        <collection name="data_collection" type="list:list" label="${tool.name} on ${on_string}: detailed output">
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)/(?P&lt;identifier_1&gt;.+)\.(?P&lt;ext&gt;[^.]+)" directory="details/" visible="false"/>
+            <filter> len(input)>1 and "details" in out_add</filter>
+        </collection>
     </outputs>
     <tests>
-        	<test>
-            		<param name="input" value="idba.fasta,Trinity.fasta" ftype="fasta" />
-			<param name="r" value="Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa" ftype="fasta" />
-			<param name="gtf" value="Saccharomyces_cerevisiae.R64-1-1.75.gtf" ftype="gtf" />
-			<param name="disable_infer_genes" value="true"/>
-			<param name="disable_infer_transcripts" value="true"/>		
-			<param name="no_plots" value="false" />
-                	<output name="short_report_txt" file="short_report.txt" lines_diff="347"/>
-                	<output name="short_report_tex" file="short_report.tex" lines_diff="347"/>
-			<output name="short_report_tsv" file="short_report.tsv" lines_diff="347"/>
-			<output_collection name="list_comparison" type="list">
-				<element name="alignment_metrics" file="alignment_metrics"/>
-				<element name="basic_metrics" file="basic_metrics"/>
-				<element name="misassemblies" file="misassemblies"/>
-				<element name="sensitivity" file="sensitivity"/>
-				<element name="specificity" file="specificity"/>
-				<element name="database_metrics" file="database_metrics"/>
-			</output_collection>
-			
-			<output_collection name="list_logs" type="list">
-				<element name="gmap.idba.err" file="logs/gmap.idba.err" compare="sim_size"/>
-				<element name="gmap.Trinity.err" file="logs/gmap.Trinity.err" compare="sim_size"/>
-				<element name="idba.blastn" file="logs/idba.blastn" compare="sim_size"/>
-				<element name="Trinity.blastn" file="logs/Trinity.blastn" compare="sim_size"/>
-				<element name="makeblastdb" file="logs/makeblastdb" compare="sim_size"/>
-				<element name="rnaQUAST" file="logs/rnaQUAST" compare="sim_size"/>
-			</output_collection>
-				
-        	</test>
-		<test>
-			<param name="input" value="spades.311.fasta" ftype="fasta" />
-			<param name="use_gtf" value="false" />
-			<param name="min_alignment" value="30" />
-			<param name="lower_threshold" value="45" />
-			<param name="upper_threshold" value="95"/>
-			<output name="short_report_pdf" file="short_report.pdf" compare="sim_size"/>
-			<output name="short_report_txt" file="short_report.txt" compare="sim_size"/>
-                	<output name="short_report_tex" file="short_report.tex" compare="sim_size"/>
-			<output name="short_report_tsv" file="short_report.tsv" compare="sim_size"/>
-			<output_collection name="list_logs" type="list">			
-				<element name="rnaQUAST" file="rnaQUAST" lines_diff="347"/>
-				<element name="spades.311.GeneMarkS_T.err" file="spades.311.GeneMarkS_T.err"/>
-			</output_collection>
-			
-		</test>
-	</tests>
+        <test>
+            <param name="input" value="idba.fasta,Trinity.fasta" ftype="fasta" />
+            <param name="r" value="Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa" ftype="fasta" />
+            <conditional name="gene_coordinates">
+                <param name="use_gtf" value="true" />
+                <param name="gtf" value="Saccharomyces_cerevisiae.R64-1-1.75.gtf" ftype="gtf" />
+                <param name="disable_infer_genes" value="true"/>
+                <param name="disable_infer_transcripts" value="true"/>
+            </conditional>
+            <param name="out_sr" value="txt,tex,tsv" />
+            <param name="out_add" value="logs,comparison,plots,details" />
+            <output name="short_report_txt" file="short_report.txt" lines_diff="347"/>
+            <output name="short_report_tex" file="short_report.tex" lines_diff="347"/>
+            <output name="short_report_tsv" file="short_report.tsv" lines_diff="347"/>
+            <output_collection name="list_comparison_png" type="list">
+                <element name="alignment_multiplicity" file="test-data/plots/alignment_multiplicity.png"/>
+                <element name="alignments_per_isoform" file="test-data/plots/alignments_per_isoform.png"/>
+                <element name="block_length" file="test-data/plots/block_length.png"/>
+                <element name="blocks_per_alignment" file="test-data/plots/blocks_per_alignment.png"/>
+                <element name="mismatch_rate" file="test-data/plots/mismatch_rate.png"/>
+                <element name="NAx" file="test-data/plots/NAx.png"/>
+                <element name="Nx" file="test-data/plots/Nx.png"/>
+                <element name="transcript_length" file="test-data/plots/transcript_length.png"/>
+                <element name="x-aligned" file="test-data/plots/x-aligned.png"/>
+                <element name="x-assembled_exons" file="test-data/plots/x-assembled_exons.png"/>
+                <element name="x-assembled" file="test-data/plots/x-assembled.png"/>
+                <element name="x-covered_exons" file="test-data/plots/x-covered_exons.png"/>
+                <element name="x-covered" file="test-data/plots/x-covered.png"/>
+                <element name="x-matched_blocks" file="test-data/plots/x-matched_blocks.png"/>
+                <element name="x-matched" file="test-data/plots/x-matched.png"/>
+            </output_collection>
+            <output_collection name="list_comparison" type="list">
+                <element name="alignment_metrics" file="alignment_metrics"/>
+                <element name="basic_metrics" file="basic_metrics"/>
+                <element name="misassemblies" file="misassemblies"/>
+                <element name="sensitivity" file="sensitivity"/>
+                <element name="specificity" file="specificity"/>
+                <element name="database_metrics" file="database_metrics"/>
+            </output_collection>
+            <output_collection name="list_logs" type="list">
+                <element name="gmap_build.err" file="logs/gmap_build.err.log" compare="sim_size"/>
+                <element name="gmap_build.out" file="logs/gmap_build.out.log" compare="sim_size"/>
+                <element name="gmap.idba.err" file="logs/gmap.idba.err.log" compare="sim_size"/>
+                <element name="gmap.Trinity.err" file="logs/gmap.Trinity.err.log" compare="sim_size"/>
+                <element name="idba.blastn" file="logs/idba.blastn.log" compare="sim_size"/>
+                <element name="Trinity.blastn" file="logs/Trinity.blastn.log" compare="sim_size"/>
+                <element name="makeblastdb" file="logs/makeblastdb.log" compare="sim_size"/>
+                <element name="rnaQUAST" file="logs/rnaQUAST.log" compare="sim_size"/>
+            </output_collection>
+            <output_collection name="data_collection" type="list:list">
+                <element name="idba">
+                    <element name="alignment_metrics" file="idba/alignment_metrics.txt"/>
+                </element>
+                <element name="Trinity">
+                    <element name="alignment_metrics" file="Trinity/alignment_metrics.txt"/>
+                </element>
+            </output_collection>
+        </test>
+        <test>
+            <param name="input" value="spades.311.fasta" ftype="fasta" />
+            <conditional name="gene_coordinates">
+                <param name="use_gtf" value="false" />
+            </conditional>
+            <param name="min_alignment" value="30" />
+            <param name="lower_threshold" value="45" />
+            <param name="upper_threshold" value="95"/>
+            <param name="out_sr" value="txt,tex,tsv,pdf" />
+            <param name="out_add" value="logs" />
+            <output name="short_report_pdf" file="short_report.pdf" compare="sim_size"/>
+            <output name="short_report_txt" file="short_report.txt" compare="sim_size"/>
+            <output name="short_report_tex" file="short_report.tex" compare="sim_size"/>
+            <output name="short_report_tsv" file="short_report.tsv" compare="sim_size"/>
+            <output_collection name="list_logs" type="list">
+                <element name="rnaQUAST" file="rnaQUAST" lines_diff="347"/>
+                <element name="spades.311.GeneMarkS_T.err" file="spades.311.GeneMarkS_T.err"/>
+            </output_collection>
+            <output_collection name="data_collection" type="list:list">
+                <element name="spades.311">
+                    <element name="alignment_metrics" file="spades.311/alignment_metrics.txt"/>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
     <help><![CDATA[
-	**What it does**
-	rnaQUAST: a quality assessment tool for de novo transcriptome assemblies
+    **What it does**
+    rnaQUAST: a quality assessment tool for de novo transcriptome assemblies
 
-	rnaQUAST—a tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. rnaQUAST calculates various metrics that demonstrate completeness and correctness levels of the assembled transcripts, and outputs them in a user-friendly report.
-	
-	**Using rnaQuast without reference**
-	you wont get: 
-	-x_assebled PNG & Txt
-	- x_assembled Exons PNG & Txt
-	- Alignments per Isoform PNG & Txt
-	- x_covered PNG & Txt
-	- x_covered Exons PNG & Txt
-	- x_matched PNG & Txt
-	- x_matched PNG & Txt
-	- x_matched Blocks PNG & Txt
-	- gmap build out log
-	- gmap build err log
-	
-	**Using rnaQuast with reference**
-	you will get:
-	- PDF report
-	- TXT report
-	- TSV report
-	- Log
-	- Alignement Metrics
-	- Basic Metrics
-	- Misassemblies
-	- Specificity
-	- Sensitivity
-	- Alignment multiplicity
-	- Block lentgh
-	- Blocks per alignment
-	- Mismatch rate
-	- Transcript length
-	- x_aligned
-	- Transcript Length PNG
-	- Nx PNG
-	- Block length PNG
-	- Blocks per alignment PNG
-	- gmap build out log
-	- gmap build err log
-	
-	**Using rnaQuast without gene coordinates**
-	you wont get: 
-	- x_assebled PNG & Txt
-	- x_assembled Exons PNG & Txt
-	- Alignments per Isoform PNG & Txt
-	- x_covered PNG & Txt
-	- x_covered Exons PNG & Txt
-	- x_matched PNG & Txt
-	- x_matched PNG & Txt
-	- x_matched Blocks PNG & Txt
-	- gmap build out log
-	- gmap build err log
-	- Database Metrics
-	- Alignment multiplicity PNG
-	- Mismatch rate PNG
-	- NAx PNG
-	- x_aligned PNG
+    rnaQUAST—a tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. rnaQUAST calculates various metrics that demonstrate completeness and correctness levels of the assembled transcripts, and outputs them in a user-friendly report.
+    
+    **Using rnaQuast without reference**
+    you wont get: 
+    -x_assebled PNG & Txt
+    - x_assembled Exons PNG & Txt
+    - Alignments per Isoform PNG & Txt
+    - x_covered PNG & Txt
+    - x_covered Exons PNG & Txt
+    - x_matched PNG & Txt
+    - x_matched PNG & Txt
+    - x_matched Blocks PNG & Txt
+    - gmap build out log
+    - gmap build err log
+    
+    **Using rnaQuast with reference**
+    you will get:
+    - PDF report
+    - TXT report
+    - TSV report
+    - Log
+    - Alignement Metrics
+    - Basic Metrics
+    - Misassemblies
+    - Specificity
+    - Sensitivity
+    - Alignment multiplicity
+    - Block lentgh
+    - Blocks per alignment
+    - Mismatch rate
+    - Transcript length
+    - x_aligned
+    - Transcript Length PNG
+    - Nx PNG
+    - Block length PNG
+    - Blocks per alignment PNG
+    - gmap build out log
+    - gmap build err log
+    
+    **Using rnaQuast without gene coordinates**
+    you wont get: 
+    - x_assebled PNG & Txt
+    - x_assembled Exons PNG & Txt
+    - Alignments per Isoform PNG & Txt
+    - x_covered PNG & Txt
+    - x_covered Exons PNG & Txt
+    - x_matched PNG & Txt
+    - x_matched PNG & Txt
+    - x_matched Blocks PNG & Txt
+    - gmap build out log
+    - gmap build err log
+    - Database Metrics
+    - Alignment multiplicity PNG
+    - Mismatch rate PNG
+    - NAx PNG
+    - x_aligned PNG
 
-	**Using rnaQuast with gene coordinates**
-	you will get: 
-	- PDF report
-	- TXT report
-	- TSV report
-	- Log
-	- Alignement Metrics
-	- Basic Metrics
-	- Misassemblies
-	- Specificity
-	- Sensitivity
-	- Alignment multiplicity
-	- Block lentgh
-	- Blocks per alignment
-	- Mismatch rate
-	- Transcript length
-	- x_aligned
-	- Transcript Length PNG
-	- Nx PNG
-	- Block length PNG
-	- Blocks per alignment PNG
-	- gmap build out log
-	- gmap build err log
-	- Database Metrics
-	- Alignment multiplicity PNG
-	- Mismatch rate PNG
-	- NAx PNG
-	- x_aligned PNG	
-	
+    **Using rnaQuast with gene coordinates**
+    you will get: 
+    - PDF report
+    - TXT report
+    - TSV report
+    - Log
+    - Alignement Metrics
+    - Basic Metrics
+    - Misassemblies
+    - Specificity
+    - Sensitivity
+    - Alignment multiplicity
+    - Block lentgh
+    - Blocks per alignment
+    - Mismatch rate
+    - Transcript length
+    - x_aligned
+    - Transcript Length PNG
+    - Nx PNG
+    - Block length PNG
+    - Blocks per alignment PNG
+    - gmap build out log
+    - gmap build err log
+    - Database Metrics
+    - Alignment multiplicity PNG
+    - Mismatch rate PNG
+    - NAx PNG
+    - x_aligned PNG    
+    
       **Using rnaQuast without drawing plots**
-	you wont get any PNG's and txt-files of these + the PDF report
+    you wont get any PNG's and txt-files of these + the PDF report
 
-	*Output*
-	**Reports**
+    *Output*
+    **Reports**
 
 The following text files with reports are contained in comparison_output directory and include results for all input assemblies. In addition, these reports are contained in <assembly_label>_output directories for each assembly separately.
 
@@ -267,8 +323,8 @@
     Database coverage – the total number of bases covered by reads (in all isoforms) divided by the total length of all isoforms.
     x%-covered genes / isoforms / exons – number of genes / isoforms / exons from the database that have at least x% of bases covered by all reads, where x is specified with lower_threshold /upper_threshold options (50% / 95% by default).
 
-	basic_mertics.txt
-	Basic transcripts metrics are calculated without reference genome and gene database.
+    basic_mertics.txt
+    Basic transcripts metrics are calculated without reference genome and gene database.
 
     - Transcripts – total number of assembled transcripts.
     - Transcripts > 500 bp
@@ -346,7 +402,7 @@
     - Relative x%-assembled genes / isoforms / exons – ratio between transcripts x%-assembled and reads x%-covered genes / isoforms / exons.
     - Relative x%-covered genes / isoforms / exons – ratio between transcripts x%-covered and reads x%-covered genes / isoforms / exons.
 
-	**Detailed output**
+    **Detailed output**
 
 These files are contained in <assembly_label>_output directories for each assembly separately.
 
@@ -361,7 +417,7 @@
 
     reads.x%-covered.list – IDs of the isoforms from the database that have at least x% bases covered by all reads, where x is specified with lower_threshold / upper_threshold options (50% / 95% by default).
 
-	**Plots**
+    **Plots**
 
 The following plots are similarly contained in both comparison_output directory and <assembly_label>_output directories. Please note, that most of the plots represent cumulative distributions and some plots are given in logarithmic scale.
 
@@ -376,7 +432,7 @@
     - Nx.png – Nx plot for transcripts. Nx is a maximal number N, such that the total length of all transcripts longer than N bp is at least x% of the total length of all transcripts.
     - NAx.png – Nx plot for alignments.
 
-	**Sensitivity**
+    **Sensitivity**
 
     - x-assembled.png – a histogram in which each bar represents the number of isoforms from the database that have at least x% captured by a single assembled transcript.
     - x-covered.png – a histogram in which each bar represents the number of isoforms from the database that have at least x% of bases covered by all alignments.
@@ -384,14 +440,14 @@
     - x-covered_exons.png – a histogram in which each bar represents the number of exons from the database that have at least x% of bases covered by all alignments.
     - alignments_per_isoform.png – plot showing number of transcript alignments per isoform
 
-	**Specificity**
+    **Specificity**
 
     - x-matched.png – a histogram in which each bar represents the number of transcripts that have at least x% matched to an isoform from the database.
     - x-matched_blocks.png – a histogram in which each bar represents the number of all blocks from all transcript alignments that have at least x% matched to an isoform from the database.
 
 
     ]]></help>
-       <citations>
+    <citations>
         <citation type="doi">10.1093/bioinformatics/btw218 </citation>
     </citations>
 </tool>