--- a/pureclip.xml	Tue May 29 19:07:42 2018 -0400
+++ b/pureclip.xml	Thu Jul 21 19:17:57 2022 +0000
@@ -1,7 +1,11 @@
-<tool id="pureclip" name="PureCLIP" version="1.0.4">
+<tool id="pureclip" name="PureCLIP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.01">
     <description>- HMM based peak caller designed for eCLIP/iCLIP data</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.4</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="1.0.4">pureclip</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">pureclip</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 ln -s '${target_bam_file}' target.bam && 
@@ -263,9 +267,9 @@
             <param name="cl_motif_bed_file" value="fimo_clmotif_occurences.chrM:4000-8300.bed" ftype="bed"/>
             <param name="max_motif_id" value="4"/>
             <param name="crosslink_bed_stats" value="True"/>
-            <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed"/>
-            <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.cov_CLmotifs.bed"/>
-            <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats"/>
+            <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed" compare="re_match"/>
+            <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.cov_CLmotifs.bed" compare="re_match"/>
+            <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats" compare="re_match"/>
         </test>
         <test>
             <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>

--- a/test-data/chrM:4000-8300.binding_regions.cov_CLmotifs.bed	Tue May 29 19:07:42 2018 -0400
+++ b/test-data/chrM:4000-8300.binding_regions.cov_CLmotifs.bed	Thu Jul 21 19:17:57 2022 +0000
@@ -1,48 +1,48 @@
-chrM	4291	4314	2.87655;4.57544;1.9093;52.3973;30.5686;4.69146;6.57447;60.2542;24.9111;22.4555;14.6916;	225.905	+
-chrM	4401	4404	58.7899;5.94153;	64.7314	+
-chrM	4417	4419	52.9006;78.1395;3.46575;	134.506	+
-chrM	4433	4434	7.10406;65.4345;	72.5386	+
-chrM	4445	4446	9.0675;	9.0675	+
-chrM	4823	4824	2.37396;	2.37396	+
-chrM	4840	4841	3.59728;	3.59728	+
-chrM	4896	4897	7.26981;	7.26981	+
-chrM	4909	4910	1.84891;2.16833;	4.01724	+
-chrM	4921	4922	1.7173;	1.7173	+
-chrM	4945	4955	8.86501;1.93776;4.40328;2.15768;	17.3637	+
-chrM	5314	5315	8.45847;0.181168;	8.63964	+
-chrM	5331	5332	2.65729;2.6687;	5.32599	+
-chrM	5343	5344	5.46374;5.48628;	10.95	+
-chrM	5361	5364	2.34726;0.0359933;	2.38326	+
-chrM	5374	5375	0.241802;	0.241802	+
-chrM	5455	5465	10.0936;3.90451;2.2512;4.38388;4.38348;	25.0167	+
-chrM	6010	6018	4.02774;19.8597;9.21876;19.8597;19.8597;9.21549;8.61924;1.05759;	91.718	+
-chrM	6202	6203	10.9092;	10.9092	+
-chrM	6214	6225	2.78068;0.343238;1.17331;13.6565;	17.9538	+
-chrM	6241	6253	27.4703;11.6802;12.277;12.3268;11.7805;49.9134;0.686498;5.27793;	131.413	+
-chrM	6345	6352	14.6293;3.35198;0.973817;8.67785;	27.633	+
-chrM	6372	6376	8.64682;1.1145;2.1039;2.91354;4.96066;	19.7394	+
-chrM	6412	6413	1.97814;	1.97814	+
-chrM	6430	6438	3.93886;1.49557;1.81725;3.14121;	10.3929	+
-chrM	6451	6453	10.4438;3.33301;	13.7768	+
-chrM	6469	6473	5.47678;0.685062;	6.16184	+
-chrM	6488	6497	0.700916;0.671846;21.8827;1.01619;1.01644;	25.2881	+
-chrM	6546	6562	9.57336;5.16057;13.9491;3.55403;0.6238;4.95052;	37.8114	+
-chrM	6637	6640	10.3353;10.7671;15.5213;12.5687;	49.1924	+
-chrM	6678	6682	0.818671;1.05925;7.72861;8.18387;1.80946;	19.5999	+
-chrM	7192	7193	1.45455;	1.45455	+
-chrM	7210	7211	0.79438;	0.79438	+
-chrM	7221	7222	17.4136;	17.4136	+
-chrM	7230	7231	5.31736;	5.31736	+
-chrM	7242	7243	0.495479;	0.495479	+
-chrM	7282	7283	1.13057;4.25317;	5.38374	+
-chrM	7309	7315	0.120627;1.31503;2.70833;1.53398;12.2368;12.2368;8.78236;	38.9339	+
-chrM	7679	7701	16.0725;13.6444;4.83849;7.07543;14.2109;9.51666;11.5284;4.20094;11.5889;16.2681;0.117034;11.3302;3.57763;	123.97	+
-chrM	7802	7809	4.65424;14.3051;5.08178;6.76985;4.3113;27.6012;	62.7235	+
-chrM	7836	7842	2.14601;1.25468;4.26851;7.94601;4.08522;31.4939;	51.1943	+
-chrM	7876	7877	3.85842;	3.85842	+
-chrM	7901	7902	25.4582;	25.4582	+
-chrM	7964	7968	0.476707;5.49676;6.95434;	12.9278	+
-chrM	7992	7998	2.19539;0.269487;3.33675;4.3845;2.53573;	12.7219	+
-chrM	8044	8050	2.4415;11.5628;14.8144;9.50755;0.084919;7.25686;	45.668	+
-chrM	8133	8143	4.07108;13.87;14.136;21.183;2.40429;8.54041;7.21096;0.115654;24.6698;	96.2012	+
-chrM	5843	5861	0.699158;52.1487;52.1487;10.0984;37.9219;5.25451;38.1317;0.969962;13.3358;	210.709	-
+chrM\t4291\t4314\t2.[0-9]*;4.[0-9]*;1.[0-9]*;52.[0-9]*;30.[0-9]*;4.[0-9]*;6.[0-9]*;60.[0-9]*;24.[0-9]*;22.[0-9]*;14.[0-9]*;\t225.[0-9]*\t+
+chrM\t4401\t4404\t58.[0-9]*;5.[0-9]*;\t64.[0-9]*\t+
+chrM\t4417\t4419\t52.[0-9]*;78.[0-9]*;3.[0-9]*;\t134.[0-9]*\t+
+chrM\t4433\t4434\t7.[0-9]*;65.[0-9]*;\t72.[0-9]*\t+
+chrM\t4445\t4446\t9.[0-9]*;\t9.[0-9]*\t+
+chrM\t4823\t4824\t2.[0-9]*;\t2.[0-9]*\t+
+chrM\t4840\t4841\t3.[0-9]*;\t3.[0-9]*\t+
+chrM\t4896\t4897\t7.[0-9]*;\t7.[0-9]*\t+
+chrM\t4909\t4910\t1.[0-9]*;2.[0-9]*;\t4.[0-9]*\t+
+chrM\t4921\t4922\t1.[0-9]*;\t1.[0-9]*\t+
+chrM\t4945\t4955\t8.[0-9]*;1.[0-9]*;4.[0-9]*;2.[0-9]*;\t17.[0-9]*\t+
+chrM\t5314\t5315\t8.[0-9]*;0.[0-9]*;\t8.[0-9]*\t+
+chrM\t5331\t5332\t2.[0-9]*;2.[0-9]*;\t5.[0-9]*\t+
+chrM\t5343\t5344\t5.[0-9]*;5.[0-9]*;\t10.[0-9]*\t+
+chrM\t5361\t5364\t2.[0-9]*;0.[0-9]*;\t2.[0-9]*\t+
+chrM\t5374\t5375\t0.[0-9]*;\t0.[0-9]*\t+
+chrM\t5455\t5465\t10.[0-9]*;3.[0-9]*;2.[0-9]*;4.[0-9]*;4.[0-9]*;\t25.[0-9]*\t+
+chrM\t6010\t6018\t4.[0-9]*;19.[0-9]*;9.[0-9]*;19.[0-9]*;19.[0-9]*;9.[0-9]*;8.[0-9]*;1.[0-9]*;\t91.[0-9]*\t+
+chrM\t6202\t6203\t10.[0-9]*;\t10.[0-9]*\t+
+chrM\t6214\t6225\t2.[0-9]*;0.[0-9]*;1.[0-9]*;13.[0-9]*;\t17.[0-9]*\t+
+chrM\t6241\t6253\t27.[0-9]*;11.[0-9]*;12.[0-9]*;12.[0-9]*;11.[0-9]*;49.[0-9]*;0.[0-9]*;5.[0-9]*;\t131.[0-9]*\t+
+chrM\t6345\t6352\t14.[0-9]*;3.[0-9]*;0.[0-9]*;8.[0-9]*;\t27.[0-9]*\t+
+chrM\t6372\t6376\t8.[0-9]*;1.[0-9]*;2.[0-9]*;2.[0-9]*;4.[0-9]*;\t19.[0-9]*\t+
+chrM\t6412\t6413\t1.[0-9]*;\t1.[0-9]*\t+
+chrM\t6430\t6438\t3.[0-9]*;1.[0-9]*;1.[0-9]*;3.[0-9]*;\t10.[0-9]*\t+
+chrM\t6451\t6453\t10.[0-9]*;3.[0-9]*;\t13.[0-9]*\t+
+chrM\t6469\t6473\t5.[0-9]*;0.[0-9]*;\t6.[0-9]*\t+
+chrM\t6488\t6497\t0.[0-9]*;0.[0-9]*;21.[0-9]*;1.[0-9]*;1.[0-9]*;\t25.[0-9]*\t+
+chrM\t6546\t6562\t9.[0-9]*;5.[0-9]*;13.[0-9]*;3.[0-9]*;0.[0-9]*;4.[0-9]*;\t37.[0-9]*\t+
+chrM\t6637\t6640\t10.[0-9]*;10.[0-9]*;15.[0-9]*;12.[0-9]*;\t49.[0-9]*\t+
+chrM\t6678\t6682\t0.[0-9]*;1.[0-9]*;7.[0-9]*;8.[0-9]*;1.[0-9]*;\t19.[0-9]*\t+
+chrM\t7192\t7193\t1.[0-9]*;\t1.[0-9]*\t+
+chrM\t7210\t7211\t0.[0-9]*;\t0.[0-9]*\t+
+chrM\t7221\t7222\t17.[0-9]*;\t17.[0-9]*\t+
+chrM\t7230\t7231\t5.[0-9]*;\t5.[0-9]*\t+
+chrM\t7242\t7243\t0.[0-9]*;\t0.[0-9]*\t+
+chrM\t7282\t7283\t1.[0-9]*;4.[0-9]*;\t5.[0-9]*\t+
+chrM\t7309\t7315\t0.[0-9]*;1.[0-9]*;2.[0-9]*;1.[0-9]*;12.[0-9]*;12.[0-9]*;8.[0-9]*;\t38.[0-9]*\t+
+chrM\t7679\t7701\t16.[0-9]*;13.[0-9]*;4.[0-9]*;7.[0-9]*;14.[0-9]*;9.[0-9]*;11.[0-9]*;4.[0-9]*;11.[0-9]*;16.[0-9]*;0.[0-9]*;11.[0-9]*;3.[0-9]*;\t123.[0-9]*\t+
+chrM\t7802\t7809\t4.[0-9]*;14.[0-9]*;5.[0-9]*;6.[0-9]*;4.[0-9]*;27.[0-9]*;\t62.[0-9]*\t+
+chrM\t7836\t7842\t2.[0-9]*;1.[0-9]*;4.[0-9]*;7.[0-9]*;4.[0-9]*;31.[0-9]*;\t51.[0-9]*\t+
+chrM\t7876\t7877\t3.[0-9]*;\t3.[0-9]*\t+
+chrM\t7901\t7902\t25.[0-9]*;\t25.[0-9]*\t+
+chrM\t7964\t7968\t0.[0-9]*;5.[0-9]*;6.[0-9]*;\t12.[0-9]*\t+
+chrM\t7992\t7998\t2.[0-9]*;0.[0-9]*;3.[0-9]*;4.[0-9]*;2.[0-9]*;\t12.[0-9]*\t+
+chrM\t8044\t8050\t2.[0-9]*;11.[0-9]*;14.[0-9]*;9.[0-9]*;0.[0-9]*;7.[0-9]*;\t45.[0-9]*\t+
+chrM\t8133\t8143\t4.[0-9]*;13.[0-9]*;14.[0-9]*;21.[0-9]*;2.[0-9]*;8.[0-9]*;7.[0-9]*;0.[0-9]*;24.[0-9]*;\t96.[0-9]*\t+
+chrM\t5843\t5861\t0.[0-9]*;52.[0-9]*;52.[0-9]*;10.[0-9]*;37.[0-9]*;5.[0-9]*;38.[0-9]*;0.[0-9]*;13.[0-9]*;\t210.[0-9]*\t-

--- a/test-data/chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed	Tue May 29 19:07:42 2018 -0400
+++ b/test-data/chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed	Thu Jul 21 19:17:57 2022 +0000
@@ -1,175 +1,175 @@
-chrM	4291	4292	3	2.87655	+
-chrM	4292	4293	3	4.57544	+
-chrM	4295	4296	3	1.9093	+
-chrM	4300	4301	3	52.3973	+
-chrM	4301	4302	3	30.5686	+
-chrM	4302	4303	3	4.69146	+
-chrM	4303	4304	3	6.57447	+
-chrM	4311	4312	3	60.2542	+
-chrM	4312	4313	3	24.9111	+
-chrM	4313	4314	3	22.4555	+
-chrM	4314	4315	3	14.6916	+
-chrM	4401	4402	3	58.7899	+
-chrM	4404	4405	3	5.94153	+
-chrM	4417	4418	3	52.9006	+
-chrM	4418	4419	3	78.1395	+
-chrM	4419	4420	3	3.46575	+
-chrM	4433	4434	3	7.10406	+
-chrM	4434	4435	3	65.4345	+
-chrM	4445	4446	3	9.0675	+
-chrM	4823	4824	3	2.37396	+
-chrM	4840	4841	3	3.59728	+
-chrM	4896	4897	3	7.26981	+
-chrM	4909	4910	3	1.84891	+
-chrM	4910	4911	3	2.16833	+
-chrM	4921	4922	3	1.7173	+
-chrM	4945	4946	3	8.86501	+
-chrM	4947	4948	3	1.93776	+
-chrM	4952	4953	3	4.40328	+
-chrM	4955	4956	3	2.15768	+
-chrM	5314	5315	3	8.45847	+
-chrM	5315	5316	3	0.181168	+
-chrM	5331	5332	3	2.65729	+
-chrM	5332	5333	3	2.6687	+
-chrM	5343	5344	3	5.46374	+
-chrM	5344	5345	3	5.48628	+
-chrM	5361	5362	3	2.34726	+
-chrM	5364	5365	3	0.0359933	+
-chrM	5374	5375	3	0.241802	+
-chrM	5455	5456	3	10.0936	+
-chrM	5456	5457	3	3.90451	+
-chrM	5457	5458	3	2.2512	+
-chrM	5464	5465	3	4.38388	+
-chrM	5465	5466	3	4.38348	+
-chrM	6010	6011	3	4.02774	+
-chrM	6011	6012	3	19.8597	+
-chrM	6012	6013	3	9.21876	+
-chrM	6013	6014	3	19.8597	+
-chrM	6014	6015	3	19.8597	+
-chrM	6015	6016	3	9.21549	+
-chrM	6016	6017	3	8.61924	+
-chrM	6018	6019	3	1.05759	+
-chrM	6202	6203	3	10.9092	+
-chrM	6214	6215	3	2.78068	+
-chrM	6216	6217	3	0.343238	+
-chrM	6217	6218	3	1.17331	+
-chrM	6225	6226	3	13.6565	+
-chrM	6241	6242	3	27.4703	+
-chrM	6246	6247	3	11.6802	+
-chrM	6247	6248	3	12.277	+
-chrM	6248	6249	3	12.3268	+
-chrM	6249	6250	3	11.7805	+
-chrM	6251	6252	3	49.9134	+
-chrM	6252	6253	3	0.686498	+
-chrM	6253	6254	3	5.27793	+
-chrM	6345	6346	3	14.6293	+
-chrM	6346	6347	3	3.35198	+
-chrM	6351	6352	3	0.973817	+
-chrM	6352	6353	3	8.67785	+
-chrM	6372	6373	3	8.64682	+
-chrM	6373	6374	3	1.1145	+
-chrM	6374	6375	3	2.1039	+
-chrM	6375	6376	3	2.91354	+
-chrM	6376	6377	3	4.96066	+
-chrM	6412	6413	3	1.97814	+
-chrM	6430	6431	3	3.93886	+
-chrM	6435	6436	3	1.49557	+
-chrM	6437	6438	3	1.81725	+
-chrM	6438	6439	3	3.14121	+
-chrM	6451	6452	3	10.4438	+
-chrM	6453	6454	3	3.33301	+
-chrM	6469	6470	3	5.47678	+
-chrM	6473	6474	3	0.685062	+
-chrM	6488	6489	3	0.700916	+
-chrM	6490	6491	3	0.671846	+
-chrM	6493	6494	3	21.8827	+
-chrM	6495	6496	3	1.01619	+
-chrM	6497	6498	3	1.01644	+
-chrM	6546	6547	3	9.57336	+
-chrM	6547	6548	3	5.16057	+
-chrM	6551	6552	3	13.9491	+
-chrM	6557	6558	3	3.55403	+
-chrM	6558	6559	3	0.6238	+
-chrM	6562	6563	3	4.95052	+
-chrM	6637	6638	3	10.3353	+
-chrM	6638	6639	3	10.7671	+
-chrM	6639	6640	3	15.5213	+
-chrM	6640	6641	3	12.5687	+
-chrM	6678	6679	3	0.818671	+
-chrM	6679	6680	3	1.05925	+
-chrM	6680	6681	3	7.72861	+
-chrM	6681	6682	3	8.18387	+
-chrM	6682	6683	3	1.80946	+
-chrM	7192	7193	3	1.45455	+
-chrM	7210	7211	3	0.79438	+
-chrM	7221	7222	3	17.4136	+
-chrM	7230	7231	3	5.31736	+
-chrM	7242	7243	3	0.495479	+
-chrM	7282	7283	3	1.13057	+
-chrM	7283	7284	3	4.25317	+
-chrM	7309	7310	3	0.120627	+
-chrM	7310	7311	3	1.31503	+
-chrM	7311	7312	3	2.70833	+
-chrM	7312	7313	3	1.53398	+
-chrM	7313	7314	3	12.2368	+
-chrM	7314	7315	3	12.2368	+
-chrM	7315	7316	3	8.78236	+
-chrM	7679	7680	3	16.0725	+
-chrM	7681	7682	3	13.6444	+
-chrM	7682	7683	3	4.83849	+
-chrM	7683	7684	3	7.07543	+
-chrM	7684	7685	3	14.2109	+
-chrM	7685	7686	3	9.51666	+
-chrM	7686	7687	3	11.5284	+
-chrM	7690	7691	3	4.20094	+
-chrM	7691	7692	3	11.5889	+
-chrM	7692	7693	3	16.2681	+
-chrM	7694	7695	3	0.117034	+
-chrM	7695	7696	3	11.3302	+
-chrM	7701	7702	3	3.57763	+
-chrM	7802	7803	3	4.65424	+
-chrM	7803	7804	3	14.3051	+
-chrM	7804	7805	3	5.08178	+
-chrM	7805	7806	3	6.76985	+
-chrM	7808	7809	3	4.3113	+
-chrM	7809	7810	3	27.6012	+
-chrM	7836	7837	3	2.14601	+
-chrM	7837	7838	3	1.25468	+
-chrM	7838	7839	3	4.26851	+
-chrM	7840	7841	3	7.94601	+
-chrM	7841	7842	3	4.08522	+
-chrM	7842	7843	3	31.4939	+
-chrM	7876	7877	3	3.85842	+
-chrM	7901	7902	3	25.4582	+
-chrM	7964	7965	3	0.476707	+
-chrM	7965	7966	3	5.49676	+
-chrM	7968	7969	3	6.95434	+
-chrM	7992	7993	3	2.19539	+
-chrM	7995	7996	3	0.269487	+
-chrM	7996	7997	3	3.33675	+
-chrM	7997	7998	3	4.3845	+
-chrM	7998	7999	3	2.53573	+
-chrM	8044	8045	3	2.4415	+
-chrM	8045	8046	3	11.5628	+
-chrM	8046	8047	3	14.8144	+
-chrM	8047	8048	3	9.50755	+
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-chrM	8050	8051	3	7.25686	+
-chrM	8133	8134	3	4.07108	+
-chrM	8134	8135	3	13.87	+
-chrM	8135	8136	3	14.136	+
-chrM	8136	8137	3	21.183	+
-chrM	8138	8139	3	2.40429	+
-chrM	8139	8140	3	8.54041	+
-chrM	8140	8141	3	7.21096	+
-chrM	8141	8142	3	0.115654	+
-chrM	8143	8144	3	24.6698	+
-chrM	5860	5861	3	0.699158	-
-chrM	5859	5860	3	52.1487	-
-chrM	5858	5859	3	52.1487	-
-chrM	5857	5858	3	10.0984	-
-chrM	5855	5856	3	37.9219	-
-chrM	5851	5852	3	5.25451	-
-chrM	5849	5850	3	38.1317	-
-chrM	5844	5845	3	0.969962	-
-chrM	5843	5844	3	13.3358	-
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--- a/test-data/chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats	Tue May 29 19:07:42 2018 -0400
+++ b/test-data/chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats	Thu Jul 21 19:17:57 2022 +0000
@@ -1,7 +1,7 @@
-gamma1.theta	0.24151
-gamma1.k	1
-gamma1.tp	0.00807885
-gamma2.theta	0.458315
-gamma2.k	3.28001
-gamma2.tp	0.00807885
-options.useKdeThreshold	0.00807885
+gamma1.theta\t[.0-9]+
+gamma1.k\t[.0-9]+
+gamma1.tp\t[.0-9]+
+gamma2.theta\t[.0-9]+
+gamma2.k\t[.0-9]+
+gamma2.tp\t[.0-9]+
+options.useKdeThreshold\t[.0-9]+