diff hicup_hicup.xml @ 7:68fb19094f84 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 398a2e3e845ada656b3a7e0a6542e1668a8bcf17

--- a/hicup_hicup.xml	Mon Oct 24 16:16:20 2022 +0000
+++ b/hicup_hicup.xml	Thu Feb 23 18:04:00 2023 +0000
@@ -85,6 +85,7 @@
             <data name="wrong_size_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*wrong_size.filter.bam" label="wrong_size.filter.bam"/>
             <data name="filter_piechart" format="svg" from_work_dir="*filter_piechart.svg" label="Filter piechart" />
             <data name="ditag_size_distribution" format="svg" from_work_dir="*.ditag_size_distribution.svg" label="Ditag size distribution" />
+            <data name="ditag_size_distribution_txt" format="tabular" from_work_dir="*.ditag_size_distribution_report.txt" label="Report of ditag size distribution" />
             <!-- Output of the deduplicator step -->
             <data name="cis_trans_piechart" format="svg" from_work_dir="*deduplicator_cis_trans_piechart.svg" label="Hicup Deduplicator Cis Trans Piechart.svg"/>
             <data name="uniques_barchart" format="svg" from_work_dir="*deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" />
@@ -107,10 +108,15 @@
             </conditional>
 
             <!-- outputs -->
-            <output name="hicup_results" file="HiCUP_summary_report.html" ftype="html" compare="sim_size"/>
+            <output name="hicup_results">
+                <assert_contents>
+                    <has_size value="4681214" delta="400000"/>
+                    <has_text text="HiCUP Summary Report"/>
+                </assert_contents>
+            </output>
             <output name="dataset_hicup" file="dataset1_2.hicup.bam" compare="sim_size" ftype="qname_sorted.bam" />
-            <output name="hicup_report" file="HiCUP_summary_report.txt" lines_diff="0"/>
-            <output name="digester_file" file="digester_file.txt" lines_diff="0"/>
+            <output name="hicup_report" file="HiCUP_summary_report_aQdQORylpl_22-59-39_22-02-2023.txt" lines_diff="0"/>
+            <output name="digester_file" file="digest_file.txt" lines_diff="0"/>
 
             <output_collection name="intermediate_results">
                 <!-- truncater step-->
@@ -122,8 +128,8 @@
                 </element>
                 <element name="dataset1_trunc" file="dataset1.trunc.fastq.gz" decompress="true"/>
                 <element name="dataset2_trunc" file="dataset2.trunc.fastq.gz" decompress="true"/>
-                <element name="dataset1_truncater_barchart" file="dataset1.truncation_barchart.svg" ftype="svg" compare="sim_size" />
-                <element name="dataset2_truncater_barchart" file="dataset2.truncation_barchart.svg" ftype="svg" compare="sim_size" />
+                <element name="dataset1_truncater_barchart" file="dataset1.fastq.truncation_barchart.svg" ftype="svg" compare="sim_size" />
+                <element name="dataset2_truncater_barchart" file="dataset2.fastq.truncation_barchart.svg" ftype="svg" compare="sim_size" />
 
                 <!-- mapper step -->
                 <element name="hicup_mapper_summary">
@@ -132,9 +138,9 @@
                         <has_text_matching expression="\s+99742\s+2476\s+2.5\s+3725\s+3.7\s+12679\s+12.7\s+80862\s+81.1\s+1143\s+1.1"/>
                     </assert_contents>
                 </element>
-                <element name="result_pair" file="dataset1_2.pair.bam" lines_diff="5" ftype="qname_sorted.bam"/>
-                <element name="dataset1_mapper_barchart" file="dataset1.mapper_barchart.svg" ftype="svg" compare="sim_size" />
-                <element name="dataset2_mapper_barchart" file="dataset2.mapper_barchart.svg" ftype="svg" compare="sim_size" />
+                <element name="result_pair" file="dataset1_2.pair.bam" lines_diff="2" ftype="qname_sorted.bam"/>
+                <element name="dataset1_mapper_barchart" file="dataset1.trunc.fastq.gz.mapper_barchart.svg" ftype="svg" compare="sim_size" />
+                <element name="dataset2_mapper_barchart" file="dataset2.trunc.fastq.gz.mapper_barchart.svg" ftype="svg" compare="sim_size" />
 
                 <!-- filter step-->
                 <element name="hicup_filter_summary">
@@ -142,15 +148,16 @@
                         <has_text_matching expression="\s+1143\s+544\s+44\s+440\s+60\s+599\s+21\s+73\s+466\s+39\s+0\s+0"/>
                     </assert_contents>
                 </element>
-                <element name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="14" ftype="qname_sorted.bam" />
-                <element name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="14" ftype="qname_sorted.bam" />
-                <element name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="14" ftype="qname_sorted.bam" />
-                <element name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="14" ftype="qname_sorted.bam" />
-                <element name="invalid_filter" file="dataset1_2_invalid.filter.bam"  lines_diff="14" ftype="qname_sorted.bam" />
-                <element name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="14" ftype="qname_sorted.bam" />
-                <element name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="14" ftype="qname_sorted.bam" />
+                <element name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="4" ftype="qname_sorted.bam" />
+                <element name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="4" ftype="qname_sorted.bam" />
+                <element name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="4" ftype="qname_sorted.bam" />
+                <element name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="4" ftype="qname_sorted.bam" />
+                <element name="invalid_filter" file="dataset1_2_invalid.filter.bam"  lines_diff="4" ftype="qname_sorted.bam" />
+                <element name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="4" ftype="qname_sorted.bam" />
+                <element name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="4" ftype="qname_sorted.bam" />
                 <element name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" compare="sim_size" />
                 <element name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" compare="sim_size" />
+                <element name="ditag_size_distribution_txt" file="dataset1_2.ditag_size_distribution_report.txt" ftype="tabular"/>
 
                 <!-- deduplicator step-->
                 <element name="cis_trans_piechart" file="dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg" ftype="svg" compare="sim_size" />