Repository 'rnaquast'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/rnaquast

Changeset 3:a9edbe21bf47 (2022-01-14)
Previous changeset 2:96f74538896e (2021-10-19) Next changeset 4:f9f2ad782d8f (2022-01-20)
Commit message:
"planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
modified:
rna_quast.xml
b
diff -r 96f74538896e -r a9edbe21bf47 rna_quast.xml
--- a/rna_quast.xml Tue Oct 19 11:02:19 2021 +0000
+++ b/rna_quast.xml Fri Jan 14 18:42:15 2022 +0000
[
b'@@ -1,10 +1,11 @@\n-<tool id="rna_quast" name="rnaQUAST" version="@TOOL_VERSION@">\n-    <description>A Quality Assessment Tool for De Novo Transcriptome Assemblies</description>\n+<tool id="rna_quast" name="rnaQUAST" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n+    <description>A quality assessment tool for De Novo transcriptome assemblies</description>\n     <xrefs>\n         <xref type="bio.tools">rnaQUAST</xref>\n     </xrefs>\n     <macros>\n         <token name="@TOOL_VERSION@">2.2.1</token>\n+        <token name="@VERSION_SUFFIX@">1</token>\n         <xml name="element_matching_line" token_name="" token_expression="">\n             <element name="@NAME@">\n                 <assert_contents>\n@@ -92,7 +93,7 @@\n     </stdio>\n     <command detect_errors="exit_code"><![CDATA[\n     #import re\n-    #for $i in $in_fasta\n+    #for $i in $transcripts\n         ln -s \'$i\' \'${re.sub(\'[^\\w\\-.]\', \'_\', i.element_identifier)}\' &&\n     #end for\n     #if $r\n@@ -109,7 +110,7 @@\n     rnaQUAST.py\n     --threads \\${GALAXY_SLOTS:-1}\n     --transcripts\n-    #for $i in $in_fasta\n+    #for $i in $transcripts\n          \'${re.sub(\'[^\\w\\-.]\', \'_\', i.element_identifier)}\'\n     #end for\n     $strand_specific\n@@ -133,8 +134,10 @@\n         --no_plots\n     #end if\n     $blat\n-    $busco_lineage\n-    ##GeneMarkS-T is not available in conda $gene_mark\n+    #if $busco_option.busco == \'true\'\n+        --busco $busco_option.lineage\n+    #end if\n+    ##$gene_mark\n     $meta\n     --lower_threshold $lower_threshold\n     --upper_threshold $upper_threshold\n@@ -145,7 +148,7 @@\n     ## move per outputs that are generated for each input (outputdir/ASSEMBLER_output)\n     ## to a joint dir (details) to make them discoverable\n     ## also remove "ASSEMBLER." prefixes from files (otherwise the test macros don\'t work)\n-    #for $i in $in_fasta\n+    #for $i in $transcripts\n         #set basename = os.path.splitext(re.sub(\'[^\\w\\-.]\', \'_\', $i.element_identifier))[0]\n         &&\n         (for f in \\$(find \'outputdir/\'$basename\'_output\' -type f);\n@@ -161,9 +164,10 @@\n     && true\n     ]]>    </command>\n     <inputs>\n-        <param name="in_fasta" type="data" format="fasta" multiple="true" label="Chromosomes/scaffolds file" />\n-        <param name="strand_specific" argument="-ss" type="boolean" truevalue="-ss" falsevalue="" checked="false" label="Strand-specific" />\n-        <param name="r" optional="true" argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" />\n+        <param argument="--transcripts" type="data" format="fasta" multiple="true" label="Transcripts" help="File(s) with transcripts in FASTA format."/>\n+        <param name="strand_specific" argument="-ss" type="boolean" truevalue="-ss" falsevalue="" checked="false" label="Strand-specific" \n+            help="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"/>\n+        <param name="r" optional="true" argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" help="File with reference genome containing all chromosomes/scaffolds in FASTA forma." />\n         <conditional name="gene_coordinates">\n             <param name="use_gtf" type="select" label="Use file with gene coordinates in GTF/GFF format?" help="We recommend to use files downloaded from GENCODE or Ensembl.">\n                 <option value="true" selected="true">Yes</option>\n@@ -171,20 +175,37 @@\n             </param>\n             <when value="true">\n                 <param name="gtf" argument="--gtf" type="data" format="gtf,gff,gff3" multiple="true" label="GTF/GFF file" />\n-                <param argument="--disable_infer_genes" type="boolean" truevalue="--disable_infer_genes" falsevalue="" checked="false" label=" GTF file contains genes records?" />\n-                <param argument="--disable_infer_transcripts" type="boolean" truevalue="--disable_infer_transcripts" falsevalue="" checked="false" label="GTF '..b'          more than 1 input for transcripts (for 1 its a HDA, for more list or HDAs) -->\n         <collection name="comparison_png" type="list" label="${tool.name} on ${on_string}: comparison plots">\n             <discover_datasets ext="png" pattern="(?P&lt;name&gt;.+)\\.png" directory="outputdir/comparison_output/" visible="false" recurse="true" />\n-            <filter> isinstance(in_fasta, list) and "plots" in out_add</filter>\n+            <filter> isinstance(transcripts, list) and "plots" in out_add</filter>\n         </collection>\n         <collection name="comparison" type="list" label="${tool.name} on ${on_string}: comparison">\n             <discover_datasets ext="txt" pattern="(?P&lt;name&gt;.+)\\.txt" directory="outputdir/comparison_output/" visible="false" recurse="true" />\n-            <filter> isinstance(in_fasta, list) and "comparison" in out_add</filter>\n+            <filter> isinstance(transcripts, list) and "comparison" in out_add</filter>\n         </collection>\n         <collection name="details" type="list:list" label="${tool.name} on ${on_string}: detailed output">\n             <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)_____(?P&lt;identifier_1&gt;.+)\\.(?P&lt;ext&gt;txt)" directory="details/" visible="false" />\n@@ -238,7 +259,7 @@\n     </outputs>\n     <tests>\n         <test expect_num_outputs="7">\n-            <param name="in_fasta" value="idba.fasta,Trinity.fasta" ftype="fasta" />\n+            <param name="transcripts" value="idba.fasta,Trinity.fasta" ftype="fasta" />\n             <param name="r" value="Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa" ftype="fasta" />\n             <conditional name="gene_coordinates">\n                 <param name="use_gtf" value="true" />\n@@ -260,7 +281,7 @@\n             </output_collection>\n         </test>\n         <test expect_num_outputs="6">\n-            <param name="in_fasta" value="Trinity.fasta" ftype="fasta" />\n+            <param name="transcripts" value="Trinity.fasta" ftype="fasta" />\n             <conditional name="gene_coordinates">\n                 <param name="use_gtf" value="false" />\n             </conditional>\n@@ -285,6 +306,38 @@\n                 </element>\n             </output_collection>\n         </test>\n+        <test expect_num_outputs="6">\n+            <param name="transcripts" value="Trinity.fasta" ftype="fasta" />\n+            <conditional name="gene_coordinates">\n+                <param name="use_gtf" value="false" />\n+            </conditional>\n+            <param name="min_alignment" value="30" />\n+            <param name="lower_threshold" value="45" />\n+            <param name="upper_threshold" value="95" />\n+            <param name="out_sr" value="txt,tex,tsv,pdf" />\n+            <param name="out_add" value="logs,details_plots" />\n+            <conditional name="busco_option">\n+                <param name="busco" value="true"/>\n+                <param name="lineage" value="metazoa"/>\n+            </conditional>\n+            <expand macro="pdf_output_test" />\n+            <expand macro="tex_output_test" />\n+            <expand macro="tsv_output_test" />\n+            <expand macro="txt_output_test" />\n+            <output_collection name="list_logs" type="list">\n+                <expand macro="element_has_text" name="Trinity.GeneMarkS_T.err" text="" />\n+                <expand macro="element_matching_line" name="rnaQUAST" expression="Thank you for using rnaQUAST!" />\n+            </output_collection>\n+            <output_collection name="details_png" type="list:list" count="1">\n+                <element name="Trinity">\n+                    <expand macro="element_has_text" name="Nx" text="PNG" />\n+                    <expand macro="element_has_text" name="transcript_length" text="PNG" />\n+                </element>\n+            </output_collection>\n+            <assert_command>\n+                <has_text text="--busco metazoa"/>\n+            </assert_command>\n+        </test>\n     </tests>\n     <help><![CDATA[\n **What is rnaQUAST**\n'