Mercurial > repos > nilesh > rseqc

changeset 62:473382134e56 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
author iuc
date Wed, 22 Feb 2023 15:06:01 +0000
parents 5968573462fa
children 27e16a30667a
files FPKM_count.xml RPKM_saturation.xml clipping_profile.xml deletion_profile.xml insertion_profile.xml junction_annotation.xml mismatch_profile.xml read_GC.xml read_NVC.xml read_duplication.xml rseqc_macros.xml test-data/output.FPKM.xls test-data/output01.tab test-data/output02.tab tin.xml
diffstat 15 files changed, 48 insertions(+), 32 deletions(-) [+]
line wrap: on
line diff
--- a/FPKM_count.xml	Sat Dec 10 11:23:05 2022 +0000
+++ b/FPKM_count.xml	Wed Feb 22 15:06:01 2023 +0000
@@ -15,7 +15,6 @@
     <command><![CDATA[
         @BAM_SAM_INPUTS@
         FPKM_count.py -i 'input.${extension}' -o output -r '${refgene}'
-
         #if str($strand_type.strand_specific) == "pair"
             -d
             #if str($strand_type.pair_type) == "sd"
@@ -24,7 +23,6 @@
                 '1+-,1-+,2++,2--'
             #end if
         #end if
-
         #if str($strand_type.strand_specific) == "single"
             -d
             #if str($strand_type.single_type) == "s"
@@ -33,9 +31,7 @@
                 '+-,-+'
             #end if
         #end if
-
         @MULTIHITS@
-
         $onlyexonic
         --single-read="${singleread}"
         ]]>
@@ -55,14 +51,26 @@
     </inputs>
 
     <outputs>
-        <data format="xls" name="outputxls" from_work_dir="output.FPKM.xls"/>
+        <data format="tabular" name="output" from_work_dir="output.FPKM.xls" label="${tool.name} on ${on_string}: FPKM counts"/>
     </outputs>
 
     <tests>
         <test>
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
             <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
-            <output name="outputxls" file="output.FPKM.xls"/>
+            <output name="output" file="output01.tab"/>
+        </test>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
+            <conditional name="multihits_type">
+                <param name="multihits_type_selector" value="skip_multihits"/>
+                <param name="mapq" value="20"/>
+            </conditional>
+            <output name="output" file="output02.tab"/>
+            <assert_command>
+                <has_text text="--mapq=20" />
+            </assert_command>
         </test>
     </tests>
 
--- a/RPKM_saturation.xml	Sat Dec 10 11:23:05 2022 +0000
+++ b/RPKM_saturation.xml	Wed Feb 22 15:06:01 2023 +0000
@@ -51,8 +51,8 @@
 
     <outputs>
         <expand macro="pdf_output_data" filename="output.saturation.pdf" />
-        <data format="xls" name="outputxls" from_work_dir="output.eRPKM.xls" label="${tool.name} on ${on_string} (RPKM xls)"/>
-        <data format="xls" name="outputrawxls" from_work_dir="output.rawCount.xls" label="${tool.name} on ${on_string} (Raw Count xls)"/>
+        <data format="tabular" name="outputxls" from_work_dir="output.eRPKM.xls" label="${tool.name} on ${on_string}: RPKM"/>
+        <data format="tabular" name="outputrawxls" from_work_dir="output.rawCount.xls" label="${tool.name} on ${on_string}: raw count"/>
         <expand macro="rscript_output_data" filename="output.saturation.r" />
     </outputs>
 
--- a/clipping_profile.xml	Sat Dec 10 11:23:05 2022 +0000
+++ b/clipping_profile.xml	Wed Feb 22 15:06:01 2023 +0000
@@ -37,13 +37,13 @@
         <test>
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
             <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" />
-            <output name="outputxls" file="output.clipping_profile.xls" />
+            <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/>
         </test>
         <test>
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
             <param name="rscript_output" value="true" />
             <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" />
-            <output name="outputxls" file="output.clipping_profile.xls" />
+            <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/>
             <output name="outputr" file="output.clipping_profile_r" />
         </test>
     </tests>
--- a/deletion_profile.xml	Sat Dec 10 11:23:05 2022 +0000
+++ b/deletion_profile.xml	Wed Feb 22 15:06:01 2023 +0000
@@ -40,7 +40,7 @@
             <param name="read_align_length" value="101" />
             <param name="rscript_output" value="true" />
             <output name="outputpdf" file="output.deletion_profile.pdf" compare="sim_size" />
-            <output name="outputxls" file="output.deletion_profile.txt" />
+            <output name="outputxls" file="output.deletion_profile.txt" ftype="tabular"/>
             <output name="outputr" file="output.deletion_profile_r" />
         </test>
     </tests>
--- a/insertion_profile.xml	Sat Dec 10 11:23:05 2022 +0000
+++ b/insertion_profile.xml	Wed Feb 22 15:06:01 2023 +0000
@@ -38,7 +38,7 @@
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
             <param name="rscript_output" value="true" />
             <output name="outputpdf" file="output.insertion_profile.pdf" compare="sim_size" />
-            <output name="outputxls" file="output.insertion_profile.xls" />
+            <output name="outputxls" file="output.insertion_profile.xls" ftype="tabular"/>
             <output name="outputr" file="output.insertion_profile_r" />
         </test>
     </tests>
--- a/junction_annotation.xml	Sat Dec 10 11:23:05 2022 +0000
+++ b/junction_annotation.xml	Wed Feb 22 15:06:01 2023 +0000
@@ -51,7 +51,7 @@
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
             <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
             <param name="rscript_output" value="true" />
-            <output name="outputxls" file="output.junction.xls" />
+            <output name="outputxls" file="output.junction.xls" ftype="tabular"/>
             <output name="outputr" file="output.junction_plot_r" />
             <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size" />
             <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size" />
--- a/mismatch_profile.xml	Sat Dec 10 11:23:05 2022 +0000
+++ b/mismatch_profile.xml	Wed Feb 22 15:06:01 2023 +0000
@@ -39,7 +39,7 @@
             <param name="read_align_length" value="101" />
             <param name="rscript_output" value="true" />
             <output name="outputpdf" file="output.mismatch_profile.pdf" compare="sim_size" />
-            <output name="outputxls" file="output.mismatch_profile.xls"/>
+            <output name="outputxls" file="output.mismatch_profile.xls" ftype="tabular"/>
             <output name="outputr" file="output.mismatch_profile_r"/>
         </test>
     </tests>
--- a/read_GC.xml	Sat Dec 10 11:23:05 2022 +0000
+++ b/read_GC.xml	Wed Feb 22 15:06:01 2023 +0000
@@ -36,7 +36,7 @@
         <test>
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
             <param name="rscript_output" value="true" />
-            <output name="outputxls" file="output.GC.xls" />
+            <output name="outputxls" file="output.GC.xls" ftype="tabular"/>
             <output name="outputr" file="output.GC_plot_r" />
             <output name="outputpdf" file="output.GC_plot.pdf" compare="sim_size" />
         </test>
--- a/read_NVC.xml	Sat Dec 10 11:23:05 2022 +0000
+++ b/read_NVC.xml	Wed Feb 22 15:06:01 2023 +0000
@@ -38,7 +38,7 @@
         <test>
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
             <param name="rscript_output" value="true" />
-            <output name="outputxls" file="output.NVC.xls" />
+            <output name="outputxls" file="output.NVC.xls" ftype="tabular"/>
             <output name="outputr" file="output.NVC_plot_r" />
             <output name="outputpdf" file="output.NVC_plot.pdf" compare="sim_size" />
         </test>
--- a/read_duplication.xml	Sat Dec 10 11:23:05 2022 +0000
+++ b/read_duplication.xml	Wed Feb 22 15:06:01 2023 +0000
@@ -26,8 +26,8 @@
 
     <outputs>
         <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf"  label="${tool.name} on ${on_string}: plot (PDF)"/>
-        <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string}: positon (XLS)"/>
-        <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string}: sequences (XLS)"/>
+        <data format="tabular" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string}: positon"/>
+        <data format="tabular" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string}: sequences"/>
         <expand macro="rscript_output_data" filename="output.DupRate_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
     </outputs>
 
@@ -35,8 +35,8 @@
         <test>
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
             <param name="rscript_output" value="true" />
-            <output name="outputxls" file="output.pos.DupRate.xls" />
-            <output name="outputseqxls" file="output.seq.DupRate.xls" />
+            <output name="outputxls" file="output.pos.DupRate.xls" ftype="tabular"/>
+            <output name="outputseqxls" file="output.seq.DupRate.xls" ftype="tabular"/>
             <output name="outputr" file="output.DupRate_plot_r" />
             <output name="outputpdf" file="output.DupRate_plot.pdf" compare="sim_size" />
         </test>
--- a/rseqc_macros.xml	Sat Dec 10 11:23:05 2022 +0000
+++ b/rseqc_macros.xml	Wed Feb 22 15:06:01 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">5.0.1</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@GALAXY_VERSION@">20.01</token>
     <xml name="requirements">
         <requirements>
@@ -110,7 +110,7 @@
     </xml>
 
     <xml name="xls_output_data" token_filename="output.xls" token_label="${tool.name} on ${on_string}: XLS">
-        <data format="xls" name="outputxls" from_work_dir="@FILENAME@" label="@LABEL@" />
+        <data format="tabular" name="outputxls" from_work_dir="@FILENAME@" label="@LABEL@" />
     </xml>
 
     <xml name="rscript_output_data" token_filename="output.r" token_label="${tool.name} on ${on_string}: Rscript">
--- a/test-data/output.FPKM.xls	Sat Dec 10 11:23:05 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-#chrom	st	end	accession	mRNA_size	gene_strand	Frag_count	FPM	FPKM
-chr1	11873	14409	NR_046018	1652.0	+	1.0	50000.0	30266.34382566586
-chr1	14361	29370	NR_024540	1769.0	-	2.0	100000.0	56529.11249293386
-chr1	17368	17436	NR_106918	68.0	-	0.0	0.0	0.0
-chr1	17368	17436	NR_107062	68.0	-	0.0	0.0	0.0
-chr1	34610	36081	NR_026818	1130.0	-	0.0	0.0	0.0
-chr1	34610	36081	NR_026820	1130.0	-	0.0	0.0	0.0
-chr1	69090	70008	NM_001005484	918.0	+	0.0	0.0	0.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output01.tab	Wed Feb 22 15:06:01 2023 +0000
@@ -0,0 +1,8 @@
+#chrom	st	end	accession	mRNA_size	gene_strand	Frag_count	FPM	FPKM
+chr1	11873	14409	NR_046018	1652.0	+	1.0	50000.0	30266.34382566586
+chr1	14361	29370	NR_024540	1769.0	-	2.0	100000.0	56529.11249293386
+chr1	17368	17436	NR_106918	68.0	-	0.0	0.0	0.0
+chr1	17368	17436	NR_107062	68.0	-	0.0	0.0	0.0
+chr1	34610	36081	NR_026818	1130.0	-	0.0	0.0	0.0
+chr1	34610	36081	NR_026820	1130.0	-	0.0	0.0	0.0
+chr1	69090	70008	NM_001005484	918.0	+	0.0	0.0	0.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output02.tab	Wed Feb 22 15:06:01 2023 +0000
@@ -0,0 +1,8 @@
+#chrom	st	end	accession	mRNA_size	gene_strand	Frag_count	FPM	FPKM
+chr1	11873	14409	NR_046018	1652.0	+	1.0	50000.0	30266.34382566586
+chr1	14361	29370	NR_024540	1769.0	-	2.0	100000.0	56529.11249293386
+chr1	17368	17436	NR_106918	68.0	-	0.0	0.0	0.0
+chr1	17368	17436	NR_107062	68.0	-	0.0	0.0	0.0
+chr1	34610	36081	NR_026818	1130.0	-	0.0	0.0	0.0
+chr1	34610	36081	NR_026820	1130.0	-	0.0	0.0	0.0
+chr1	69090	70008	NM_001005484	918.0	+	0.0	0.0	0.0
--- a/tin.xml	Sat Dec 10 11:23:05 2022 +0000
+++ b/tin.xml	Wed Feb 22 15:06:01 2023 +0000
@@ -53,7 +53,7 @@
 
     <outputs>
         <data name="outputsummary" format="tabular" from_work_dir="summary.tab" label="TIN on ${on_string} (summary)" />
-        <data name="outputxls" format="xls" from_work_dir="tin.xls" label="TIN on ${on_string} (tin)" />
+        <data name="outputxls" format="tabular" from_work_dir="tin.xls" label="TIN on ${on_string} (tin)" />
     </outputs>
 
     <!-- PDF Files contain R version, must avoid checking for diff -->
@@ -62,7 +62,7 @@
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
             <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
             <output name="outputsummary" file="summary.tin.txt" ftype="tabular"/>
-            <output name="outputxls" file="output.tin.xls" ftype="xls"/>
+            <output name="outputxls" file="output.tin.xls" ftype="tabular"/>
         </test>
     </tests>