Mercurial > repos > bgruening > hicexplorer_hicplotviewpoint

changeset 5:67bd57e960a3 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
author iuc
date Sat, 09 Jun 2018 15:34:08 -0400
parents c4f273c3c73f
children 6cca935297f6
files hicPlotViewpoint.xml macros.xml test-data/Li_chrX30-35_cool.png test-data/Li_et_al_2015.cool test-data/distVsCounts.txt
diffstat 5 files changed, 86 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/hicPlotViewpoint.xml	Fri Apr 27 08:43:05 2018 -0400
+++ b/hicPlotViewpoint.xml	Sat Jun 09 15:34:08 2018 -0400
@@ -7,18 +7,29 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 
-        hicPlotViewpoint --matrix '$matrix_h5_cooler'
+        #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
+            ln -s '$m' ${counter}_matrix &&
+        #end for
+        #set $m = '" "'.join([ '%s_matrix' % $counter for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
+
+        hicPlotViewpoint --matrix "$m"
         #if $interactionOutFileName:
-            $interactionOutFileName interactions.bedgraph
+            $interactionOutFileName interactions
         #end if
         --outFileName plot.$image_file_format
         --region $region
         --referencePoint $referencePoint
         && mv plot.$image_file_format plot
+        && ls -lah
+        #if $interactionOutFileName:
+            #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
+                && mv interactions_${counter}_matrix.bedgraph ${counter}_interactions.bedgraph
+            #end for
+        #end if
 ]]>
     </command>
     <inputs>
-        <expand macro='matrix_h5_cooler_macro' />
+        <expand macro='matrix_h5_cooler_multiple_macro' />
         <expand macro="region" />
         <param name="referencePoint" type="text" label="Reference point"
             help="The format is chr:referencePoint or chr:regionStart-regionEnd."/>
@@ -33,34 +44,37 @@
     </inputs>
     <outputs>
 
-        <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot">
+        <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
             <change_format>
                 <when input="image_file_format" value="png" format="png" />
                 <when input="image_file_format" value="svg" format="svg" />
             </change_format>
         </data>
-        <data name='interactionFile' from_work_dir='interactions.bedgraph' format='bedgraph' label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Bedgraph">
+
+        <data format="bedgraph" name="interactionFile" >
+            <discover_datasets pattern='(?P&lt;designation&gt;.+)\_interactions\.bedgraph' directory="." visible="true"/>
             <filter>interactionOutFileName</filter>
         </data>
 
     </outputs>
     <tests>
         <test>
-            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
+            <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
             <param name="image_file_format" value="png" />
             <param name='region' value='X:3000000-3500000' />
             <param name='referencePoint' value='X:3200000' />
             <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/>
         </test>
         <test>
-            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
+            <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
             <param name="image_file_format" value="png" />
             <param name='region' value='X:3000000-3500000' />
             <param name='referencePoint' value='X:3200000-3300000' />
             <param name='interactionOutFileName' value='True' />
             <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/>
-            <output name="interactionFile" file="li_32-33mb_interactions.bedgraph" ftype="bedgraph" compare="sim_size"/>
-
+            <output name="interactionFile">
+                <discovered_dataset designation="0" file="li_32-33mb_interactions.bedgraph" />
+            </output>
         </test>
     </tests>
     <help><![CDATA[
--- a/macros.xml	Fri Apr 27 08:43:05 2018 -0400
+++ b/macros.xml	Sat Jun 09 15:34:08 2018 -0400
@@ -1,6 +1,6 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@WRAPPER_VERSION@">2.1.2</token>
+    <token name="@WRAPPER_VERSION@">2.1.4</token>
     <token name="@USE_RANGE@">
         #if $use_range.select_use_range == "yes_use_range":
             --range $range_min:$range_max
Binary file test-data/Li_chrX30-35_cool.png has changed
Binary file test-data/Li_et_al_2015.cool has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/distVsCounts.txt	Sat Jun 09 15:34:08 2018 -0400
@@ -0,0 +1,62 @@
+	Chromosome	Contacts	Distance	Matrix
+0	all	2.673662429796039	0	small_test_matrix_50kb_res.h5
+1	all	1.6689429928741093	50000	small_test_matrix_50kb_res.h5
+2	all	0.7796660703637448	100000	small_test_matrix_50kb_res.h5
+3	all	0.4811377245508982	150000	small_test_matrix_50kb_res.h5
+4	all	0.3259170174383644	200000	small_test_matrix_50kb_res.h5
+5	all	0.2530193236714976	250000	small_test_matrix_50kb_res.h5
+6	all	0.19278569263413156	300000	small_test_matrix_50kb_res.h5
+7	all	0.1475958612294583	350000	small_test_matrix_50kb_res.h5
+8	all	0.12736713500305435	400000	small_test_matrix_50kb_res.h5
+9	all	0.11737664725712535	450000	small_test_matrix_50kb_res.h5
+10	all	0.09348093480934809	500000	small_test_matrix_50kb_res.h5
+11	all	0.08145634063560629	550000	small_test_matrix_50kb_res.h5
+12	all	0.07492260061919505	600000	small_test_matrix_50kb_res.h5
+13	all	0.06803355079217148	650000	small_test_matrix_50kb_res.h5
+14	all	0.06016209476309227	700000	small_test_matrix_50kb_res.h5
+15	all	0.05411323115420707	750000	small_test_matrix_50kb_res.h5
+16	all	0.0514752040175769	800000	small_test_matrix_50kb_res.h5
+17	all	0.043464566929133856	850000	small_test_matrix_50kb_res.h5
+18	all	0.04835651074589128	900000	small_test_matrix_50kb_res.h5
+19	all	0.04281636536631779	950000	small_test_matrix_50kb_res.h5
+20	all	0.04010184595798854	1000000	small_test_matrix_50kb_res.h5
+21	all	0.034493771957840945	1050000	small_test_matrix_50kb_res.h5
+22	all	0.035256410256410256	1100000	small_test_matrix_50kb_res.h5
+23	all	0.030556449018977163	1150000	small_test_matrix_50kb_res.h5
+24	all	0.027437056165267915	1200000	small_test_matrix_50kb_res.h5
+25	all	0.030774214447683836	1250000	small_test_matrix_50kb_res.h5
+26	all	0.03153446033810143	1300000	small_test_matrix_50kb_res.h5
+27	all	0.026753670473083198	1350000	small_test_matrix_50kb_res.h5
+28	all	0.025867714472822528	1400000	small_test_matrix_50kb_res.h5
+29	all	0.028252299605781867	1450000	small_test_matrix_50kb_res.h5
+30	all	0.025379037574159526	1500000	small_test_matrix_50kb_res.h5
+31	all	0.026124338624338623	1550000	small_test_matrix_50kb_res.h5
+32	all	0.025547445255474453	1600000	small_test_matrix_50kb_res.h5
+33	all	0.0262982689747004	1650000	small_test_matrix_50kb_res.h5
+34	all	0.018036072144288578	1700000	small_test_matrix_50kb_res.h5
+35	all	0.028820375335120642	1750000	small_test_matrix_50kb_res.h5
+36	all	0.024546065904505716	1800000	small_test_matrix_50kb_res.h5
+37	all	0.025303643724696356	1850000	small_test_matrix_50kb_res.h5
+38	all	0.01963439404197698	1900000	small_test_matrix_50kb_res.h5
+39	all	0.020380434782608696	1950000	small_test_matrix_50kb_res.h5
+40	all	0.026244035446489435	2000000	small_test_matrix_50kb_res.h5
+41	all	0.024623803009575923	2050000	small_test_matrix_50kb_res.h5
+42	all	0.024365133836650652	2100000	small_test_matrix_50kb_res.h5
+43	all	0.01928374655647383	2150000	small_test_matrix_50kb_res.h5
+44	all	0.017622667588113337	2200000	small_test_matrix_50kb_res.h5
+45	all	0.015256588072122053	2250000	small_test_matrix_50kb_res.h5
+46	all	0.021224773834377174	2300000	small_test_matrix_50kb_res.h5
+47	all	0.01920391061452514	2350000	small_test_matrix_50kb_res.h5
+48	all	0.014365802382620883	2400000	small_test_matrix_50kb_res.h5
+49	all	0.014416315049226441	2450000	small_test_matrix_50kb_res.h5
+50	all	0.016231474947071278	2500000	small_test_matrix_50kb_res.h5
+51	all	0.013456090651558074	2550000	small_test_matrix_50kb_res.h5
+52	all	0.01492007104795737	2600000	small_test_matrix_50kb_res.h5
+53	all	0.020306376914855716	2650000	small_test_matrix_50kb_res.h5
+54	all	0.013576277241872096	2700000	small_test_matrix_50kb_res.h5
+55	all	0.0146900752418488	2750000	small_test_matrix_50kb_res.h5
+56	all	0.017966223499820338	2800000	small_test_matrix_50kb_res.h5
+57	all	0.017297297297297298	2850000	small_test_matrix_50kb_res.h5
+58	all	0.018070112034694615	2900000	small_test_matrix_50kb_res.h5
+59	all	0.013773106197897789	2950000	small_test_matrix_50kb_res.h5
+60	all	0.01599418393311523	3000000	small_test_matrix_50kb_res.h5