Mercurial > repos > rnateam > ribotaper

changeset 2:9dda0cc9ff98 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
author rnateam
date Wed, 30 Nov 2016 16:57:07 -0500
parents a56343c142d5
children 579b3be2559f
files ribotaper_part1_create_annotation_files.xml ribotaper_part2_create_metaplots.xml ribotaper_part3_main.xml
diffstat 3 files changed, 15 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/ribotaper_part1_create_annotation_files.xml	Tue Nov 29 14:33:00 2016 -0500
+++ b/ribotaper_part1_create_annotation_files.xml	Wed Nov 30 16:57:07 2016 -0500
@@ -34,8 +34,8 @@
                "/>
     </inputs>
     <outputs>
-        <data name="output1" type="data" format="bed" from_work_dir="annotation_path/start_stops_FAR.bed" label="start_stops_FAR"/>
-        <data name="output2" type="data" format="zip" label="annotation_path"/>
+        <data name="output1" format="bed" from_work_dir="annotation_path/start_stops_FAR.bed" label="start_stops_FAR"/>
+        <data name="output2" format="tar" label="annotation_path"/>
     </outputs>
     <tests>
         <test>
@@ -79,7 +79,7 @@
 ``Ribotaper part 1`` generates two files:
 
   - **start_stops_FAR** in BED format
-  - **annotation_path**  in format of zip
+  - **annotation_path**  in format of tar
 
 *Start_stops_FAR*
 is used as an input for ``ribotaper part 2``.
--- a/ribotaper_part2_create_metaplots.xml	Tue Nov 29 14:33:00 2016 -0500
+++ b/ribotaper_part2_create_metaplots.xml	Wed Nov 30 16:57:07 2016 -0500
@@ -31,8 +31,8 @@
         <param name="start_stops_FAR" type="data" format="bed" label="start_stops_FAR" help="Please run 'ribotaper part 1' to generate the table."/>
     </inputs>
     <outputs>
-        <data name="output1" type="data" format="pdf" from_work_dir="merged_metagene.pdf" label="Metagene analysis results for P-sites definition (figures)"/>
-        <data name="output2" type="data" format="tabular" from_work_dir="metagene" label="Metagene analysis results for P-sites definition (table)"/>
+        <data name="output1" format="pdf" from_work_dir="merged_metagene.pdf" label="Metagene analysis results for P-sites definition (figures)"/>
+        <data name="output2" format="tabular" from_work_dir="metagene" label="Metagene analysis results for P-sites definition (table)"/>
     </outputs>
     <tests>
         <test>
--- a/ribotaper_part3_main.xml	Tue Nov 29 14:33:00 2016 -0500
+++ b/ribotaper_part3_main.xml	Wed Nov 30 16:57:07 2016 -0500
@@ -23,7 +23,7 @@
 
     ]]></command>
     <inputs>
-        <param name="annotation_path" type="data" format="zip" label="annotation_path" help="Please run 'ribotaper part 1' to generate the archive."/>
+        <param name="annotation_path" type="data" format="tar" label="annotation_path" help="Please run 'ribotaper part 1' to generate the archive."/>
         <param name="ribo_bam" type="data" format="BAM" label="ribo_bam" help="Ribo-seq alignment file in BAM format."/>
         <param name="rna_bam" type="data" format="BAM" label="rna_bam" help="RNA-seq alignment file in BAM format."/>
         <param name="read_lenghts_ribo" type="text" value="26,28,29"  label="Read length" help="Read lengths, comma-separated values, which are used for P-site calculation. Example, 26,28,29.
@@ -32,18 +32,18 @@
         Please run 'ribotaper part 2' to deterimine appropriate values."/>
     </inputs>
     <outputs>
-        <data name="output1" type="data" format="pdf" from_work_dir="quality_check_plots.pdf" label="QC plots"/>
-        <data name="output2" type="data" format="tabular" from_work_dir="ORFs_genes_found" label="Summary of translated ORFs"/>
-        <data name="output3" type="data" format="tabular" from_work_dir="ORFs_max" label="Translated ORFs (max)"/>
-        <data name="output4" type="data" format="tabular" from_work_dir="ORFs_max_filt" label="Translated ORFs (max_filt)"/>
-        <data name="output5" type="data" format="bed" from_work_dir="translated_ORFs_sorted.bed" label="Translated ORFs (sorted)"/>
-        <data name="output6" type="data" format="bed" from_work_dir="translated_ORFs_filtered_sorted.bed" label="Translated ORFs (filtered/sorted)"/>
-        <data name="output7" type="data" format="fasta" from_work_dir="protein_db_max.fasta" label="Protein DB"/>
-        <data name="output8" type="data" format="pdf" from_work_dir="Final_ORF_results.pdf" label="ORF categories (length/coverage)"/>
+        <data name="output1" format="pdf" from_work_dir="quality_check_plots.pdf" label="QC plots"/>
+        <data name="output2" format="tabular" from_work_dir="ORFs_genes_found" label="Summary of translated ORFs"/>
+        <data name="output3" format="tabular" from_work_dir="ORFs_max" label="Translated ORFs (max)"/>
+        <data name="output4" format="tabular" from_work_dir="ORFs_max_filt" label="Translated ORFs (max_filt)"/>
+        <data name="output5" format="bed" from_work_dir="translated_ORFs_sorted.bed" label="Translated ORFs (sorted)"/>
+        <data name="output6" format="bed" from_work_dir="translated_ORFs_filtered_sorted.bed" label="Translated ORFs (filtered/sorted)"/>
+        <data name="output7" format="fasta" from_work_dir="protein_db_max.fasta" label="Protein DB"/>
+        <data name="output8" format="pdf" from_work_dir="Final_ORF_results.pdf" label="ORF categories (length/coverage)"/>
     </outputs>
     <tests>
         <test>
-            <param name="annotation_path" value="annotation_path.tgz" ftype="zip"/>
+            <param name="annotation_path" value="annotation_path.tgz" ftype="tar"/>
             <param name="ribo_bam" value="test_ribo.bam"/>
             <param name="rna_bam" value="test_rna.bam"/>
             <output name="output2" file="ORFs_genes_found"/>