# HG changeset patch
# User bgruening
# Date 1632425938 0
# Node ID c9e29ac5d0997feb24a5951e3da1ee6aca83d562
# Parent  477d829d32502e6bf7efc9b41d4cf33b1d070ab0
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"

diff -r 477d829d3250 -r c9e29ac5d099 cmalign.xml
--- a/cmalign.xml	Sat Nov 11 16:01:09 2017 -0500
+++ b/cmalign.xml	Thu Sep 23 19:38:58 2021 +0000
@@ -1,10 +1,11 @@
-<tool id="infernal_cmalign" name="cmalign" version="@VERSION@.0">
+<tool id="infernal_cmalign" name="cmalign" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Align sequences to a covariance model against a sequence database</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
+    <expand macro="xrefs"/>
     <command>
 <![CDATA[
 
diff -r 477d829d3250 -r c9e29ac5d099 cmbuild.xml
--- a/cmbuild.xml	Sat Nov 11 16:01:09 2017 -0500
+++ b/cmbuild.xml	Thu Sep 23 19:38:58 2021 +0000
@@ -1,11 +1,12 @@
-<tool id="infernal_cmbuild" name="cmbuild" version="@VERSION@.0">
+<tool id="infernal_cmbuild" name="cmbuild" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Build covariance models from sequence alignments</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <parallelism method="multi" split_inputs="alignment_infile" split_mode="to_size" split_size="10" merge_outputs="cmfile_outfile"></parallelism>
+    <!--parallelism method="multi" split_inputs="alignment_infile" split_mode="to_size" split_size="10" merge_outputs="cmfile_outfile"></parallelism-->
     <expand macro="requirements" />
     <expand macro="stdio" />
+    <expand macro="xrefs"/>
     <command>
 <![CDATA[
     cmbuild
@@ -38,6 +39,9 @@
             #if $effective_opts.eminseq
                 --eminseq $effective_opts.eminseq
             #end if
+            #if $effective_opts.emaxseq
+                --emaxseq $effective_opts.emaxseq
+            #end if
             #if $effective_opts.ehmmre
                 --ehmmre $effective_opts.ehmmre
             #end if
@@ -151,6 +155,9 @@
                     <param name="eminseq" type="integer" value=""
                         label="Define the minimum allowed effective sequence number" help="(--eminseq)" optional="true"/>
 
+                    <param name="emaxseq" type="integer" value=""
+                    label="Define the maximum allowed effective sequence number" help="(--emaxseq)" optional="true"/>
+
                     <param name="ehmmre" type="float" value=""
                         label="Set the target HMM mean match state relative entropy" help="(--ehmmre)" optional="true"/>
 
@@ -253,7 +260,7 @@
 
         </inputs>
     <outputs>
-        <data format="text" name="summary_outfile" label="cmbuild summary on ${on_string}">
+        <data format="txt" name="summary_outfile" label="cmbuild summary on ${on_string}">
             <filter>is_summery_output is True</filter>
         </data>
         <!--<data format="stockholm" name="annotated_source_alignment_outfile" label="Annotated alignment from ${on_string}"/>-->
@@ -324,12 +331,29 @@
                 <param name="selector" value="true"/>
                 <param name="L" value="0.1"/>
             </conditional>
-            <output name="outfile">
+            <output name="cmfile_outfile">
                 <assert_contents>
                     <has_text text="S     0    -1 0     1     4     0     1    89   109  -7.220  -8.465  -0.063  -4.919"/>
                 </assert_contents>
             </output>
         </test>
+        <!-- Test emax seq parameter -->
+        <test>
+            <param name="alignment_infile" value="cmbuild_input_tRNA5.sto"/>
+            <conditional name="Calibrate">
+                <param name="selector" value="true"/>
+                <param name="L" value="0.1"/>
+            </conditional>
+            <conditional name="effective_opts">
+                <param name="effective_opts_selector" value="--eent"/>
+                <param name="emaxseq" value="100"/>
+            </conditional>
+            <output name="cmfile_outfile">
+                <assert_contents>
+                    <has_text text="S     0    -1 0     1     4     0     1    89   109  -7.111  -8.357  -0.068  -4.810"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r 477d829d3250 -r c9e29ac5d099 cmpress.xml
--- a/cmpress.xml	Sat Nov 11 16:01:09 2017 -0500
+++ b/cmpress.xml	Thu Sep 23 19:38:58 2021 +0000
@@ -1,10 +1,11 @@
-<tool id="infernal_cmpress" name="cmpress" version="@VERSION@.0">
+<tool id="infernal_cmpress" name="cmpress" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description> Prepare a covariance model database for cmscan</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
+    <expand macro="xrefs"/>
     <command>
 <![CDATA[
     ## CM file from the history or stored as database on disc
diff -r 477d829d3250 -r c9e29ac5d099 cmscan.xml
--- a/cmscan.xml	Sat Nov 11 16:01:09 2017 -0500
+++ b/cmscan.xml	Thu Sep 23 19:38:58 2021 +0000
@@ -1,10 +1,11 @@
-<tool id="infernal_cmscan" name="cmscan" version="@VERSION@.0">
+<tool id="infernal_cmscan" name="cmscan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description> Search sequences against collections of covariance models</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
+    <expand macro="xrefs"/>
     <command>
 <![CDATA[
     ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
@@ -73,8 +74,19 @@
         #end if
         ## sequence file
         '$seqdb'
-        &&
-        sed 's/ \+ /\t/g' '\$temp_tabular_output' > '$outfile'
+        ######### Parse the output file in order to fix a problem reported in https://help.galaxyproject.org/t/messy-infernal-cmscan-output/5984
+        ## remove the header
+        && tail -n +3 '\$temp_tabular_output' > headless_file
+        ## extract the last column, since the description includes a variable number of spaces (so, is not considered as a column by awk)
+        && awk '{$1=$2=$3=$4=$5=$6=$7=$8=$9=$10=$11=$12=$13=$14=$15=$16=$17=""; print $0}' headless_file > description_column
+        ## fix the tabulation the rest content (except the description column)
+        && awk 'OFS="\t" {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,$13,$14,$15,$16,$17 > ("tabulated_columns")}' headless_file
+        ## add the description column to the tabulated data
+        && paste -d"\t" tabulated_columns description_column > joined_file
+        ## include a correct header
+        && echo -e '#target\tname\taccession\tquery name\taccession\tmdl\tmdl from\tmdl to\tseq from\tseq to\tstrand\ttrunc\tpass\tgc\tbias\tscore\tE-value\tinc\tdescription of target' > header
+        ## export the result
+        && cat header joined_file > '$outfile'
 
 ]]>
     </command>
@@ -226,12 +238,10 @@
                 label="Only search the top (Watson) strand of target sequences" help="in the sequence database"/>
 
         </section>
-
-
-
     </inputs>
     <outputs>
         <data format="tabular" name="outfile" label="cmscan on ${on_string}"/>
+
     </outputs>
     <tests>
         <test>
@@ -241,8 +251,9 @@
             </conditional>
             <param name="aux_files" value="minifam.tar" ftype="tar"/>
             <param name="seqdb" value="metag-example.fa"/>
-            <output name="outfile">
+            <output name="outfile" file="test_cmscan.tabular" ftype="tabular" lines_diff="8">
                 <assert_contents>
+                    <has_n_lines n="15"/>
                     <has_text text="AAGA01015927.1"/>
                 </assert_contents>
             </output>
diff -r 477d829d3250 -r c9e29ac5d099 cmsearch.xml
--- a/cmsearch.xml	Sat Nov 11 16:01:09 2017 -0500
+++ b/cmsearch.xml	Thu Sep 23 19:38:58 2021 +0000
@@ -1,11 +1,12 @@
-<tool id="infernal_cmsearch" name="cmsearch" version="@VERSION@.0">
+<tool id="infernal_cmsearch" name="cmsearch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Search covariance model(s) against a sequence database </description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <parallelism method="multi" split_inputs="seqdb" split_mode="to_size" split_size="500" merge_outputs="outfile,multiple_alignment_output"></parallelism>
+    <!--parallelism method="multi" split_inputs="seqdb" split_mode="to_size" split_size="500" merge_outputs="outfile,multiple_alignment_output"></parallelism-->
     <expand macro="requirements"/>
     <expand macro="stdio" />
+    <expand macro="xrefs"/>
     <command>
 <![CDATA[
         ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
@@ -24,10 +25,10 @@
             $notrunc
             $anytrunc
             $nonull3
-            #if $smxsize <> 128.0
+            #if str($smxsize) != "128.0"
                 --smxsize $smxsize
             #end if
-            #if $mxsize <> 128.0
+            #if str($mxsize) != "128.0"
                 --mxsize $mxsize
             #end if
             --tblout \$temp_tabular_output
@@ -247,7 +248,6 @@
             </conditional>
             <param name="seqdb" value="cmsearch_input2.fa"/>
             <output name="outfile" file="cmsearch_result.tabular"/>
-
         </test>
     </tests>
 
diff -r 477d829d3250 -r c9e29ac5d099 cmstat.xml
--- a/cmstat.xml	Sat Nov 11 16:01:09 2017 -0500
+++ b/cmstat.xml	Thu Sep 23 19:38:58 2021 +0000
@@ -1,10 +1,11 @@
-<tool id="infernal_cmstat" name="cmstat" version="@VERSION@.0">
+<tool id="infernal_cmstat" name="cmstat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Summary statistics for covariance model </description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <expand macro="stdio" />
+    <expand macro="xrefs"/>
     <command>
 <![CDATA[
         ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
diff -r 477d829d3250 -r c9e29ac5d099 infernal.py
--- a/infernal.py	Sat Nov 11 16:01:09 2017 -0500
+++ b/infernal.py	Thu Sep 23 19:38:58 2021 +0000
@@ -1,76 +1,88 @@
 # -*- coding: utf-8 -*-
 
-from galaxy.datatypes.data import Text
-from galaxy.datatypes.sniff import get_headers, get_test_fname
-from galaxy.datatypes.data import get_file_peek
+import logging
+import os
 import subprocess
-import os
 
+from galaxy.datatypes.data import get_file_peek, Text
 from galaxy.datatypes.metadata import MetadataElement
-from galaxy.datatypes import metadata
+
 
-def count_special_lines( word, filename, invert = False ):
+def count_special_lines(word, filename, invert=False):
     """
-        searching for special 'words' using the grep tool
-        grep is used to speed up the searching and counting
-        The number of hits is returned.
+    searching for special 'words' using the grep tool
+    grep is used to speed up the searching and counting
+    The number of hits is returned.
     """
     try:
         cmd = ["grep", "-c"]
         if invert:
-            cmd.append('-v')
+            cmd.append("-v")
         cmd.extend([word, filename])
         out = subprocess.Popen(cmd, stdout=subprocess.PIPE)
         return int(out.communicate()[0].split()[0])
-    except:
+    except Exception:
         pass
     return 0
 
-def count_lines( filename, non_empty = False):
+
+def count_lines(filename, non_empty=False):
     """
-        counting the number of lines from the 'filename' file
+    counting the number of lines from the 'filename' file
     """
     try:
         if non_empty:
-            out = subprocess.Popen(['grep', '-cve', '^\s*$', filename], stdout=subprocess.PIPE)
+            out = subprocess.Popen(
+                ["grep", "-cve", "^\s*$", filename], stdout=subprocess.PIPE  # noqa W605
+            )
         else:
-            out = subprocess.Popen(['wc', '-l', filename], stdout=subprocess.PIPE)
+            out = subprocess.Popen(["wc", "-l", filename], stdout=subprocess.PIPE)
         return int(out.communicate()[0].split()[0])
-    except:
+    except Exception:
         pass
     return 0
 
 
-class Infernal_CM_1_1( Text ):
+class Infernal_CM_1_1(Text):
     file_ext = "cm"
 
-    MetadataElement( name="number_of_models", default=0, desc="Number of covariance models", readonly=True, visible=True, optional=True, no_value=0 )
+    MetadataElement(
+        name="number_of_models",
+        default=0,
+        desc="Number of covariance models",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=0,
+    )
 
-    def set_peek( self, dataset, is_multi_byte=False ):
+    def set_peek(self, dataset, is_multi_byte=False):
         if not dataset.dataset.purged:
-            dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
-            if (dataset.metadata.number_of_models == 1):
+            dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
+            if dataset.metadata.number_of_models == 1:
                 dataset.blurb = "1 model"
             else:
                 dataset.blurb = "%s models" % dataset.metadata.number_of_models
-            dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+            dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disc"
 
-    def sniff( self, filename ):
+    def sniff(self, filename):
         if count_special_lines("^INFERNAL1/a", filename) > 0:
             return True
         else:
             return False
 
-    def set_meta( self, dataset, **kwd ):
+    def set_meta(self, dataset, **kwd):
         """
         Set the number of models in dataset.
         """
-        dataset.metadata.number_of_models = count_special_lines("^INFERNAL1/a", dataset.file_name)
+        dataset.metadata.number_of_models = count_special_lines(
+            "^INFERNAL1/a", dataset.file_name
+        )
 
-    def split( cls, input_datasets, subdir_generator_function, split_params):
+    def split(cls, input_datasets, subdir_generator_function, split_params):
         """
         Split the input files by model records.
         """
@@ -82,14 +94,17 @@
         input_files = [ds.file_name for ds in input_datasets]
 
         chunk_size = None
-        if split_params['split_mode'] == 'number_of_parts':
-            raise Exception('Split mode "%s" is currently not implemented for CM-files.' % split_params['split_mode'])
-        elif split_params['split_mode'] == 'to_size':
-            chunk_size = int(split_params['split_size'])
+        if split_params["split_mode"] == "number_of_parts":
+            raise Exception(
+                'Split mode "%s" is currently not implemented for CM-files.'
+                % split_params["split_mode"]
+            )
+        elif split_params["split_mode"] == "to_size":
+            chunk_size = int(split_params["split_size"])
         else:
-            raise Exception('Unsupported split mode %s' % split_params['split_mode'])
+            raise Exception("Unsupported split mode %s" % split_params["split_mode"])
 
-        def _read_cm_records( filename ):
+        def _read_cm_records(filename):
             lines = []
             with open(filename) as handle:
                 for line in handle:
@@ -97,32 +112,33 @@
                         yield lines
                         lines = [line]
                     else:
-                        lines.append( line )
+                        lines.append(line)
             yield lines
 
-        def _write_part_cm_file( accumulated_lines ):
+        def _write_part_cm_file(accumulated_lines):
             part_dir = subdir_generator_function()
-            part_path = os.path.join( part_dir, os.path.basename( input_files[0] ) )
-            part_file = open( part_path, 'w' )
-            part_file.writelines( accumulated_lines )
+            part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
+            part_file = open(part_path, "w")
+            part_file.writelines(accumulated_lines)
             part_file.close()
 
         try:
-            cm_records = _read_cm_records( input_files[0] )
+            cm_records = _read_cm_records(input_files[0])
             cm_lines_accumulated = []
-            for counter, cm_record in enumerate( cm_records, start = 1):
-                cm_lines_accumulated.extend( cm_record )
+            for counter, cm_record in enumerate(cm_records, start=1):
+                cm_lines_accumulated.extend(cm_record)
                 if counter % chunk_size == 0:
-                    _write_part_cm_file( cm_lines_accumulated )
+                    _write_part_cm_file(cm_lines_accumulated)
                     cm_lines_accumulated = []
             if cm_lines_accumulated:
-                _write_part_cm_file( cm_lines_accumulated )
-        except Exception,  e:
-            log.error('Unable to split files: %s' % str(e))
+                _write_part_cm_file(cm_lines_accumulated)
+        except Exception as e:
+            logging.error("Unable to split files: %s" % str(e))
             raise
+
     split = classmethod(split)
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     Infernal_CM_1_1()
-    Stockholm_1_0()
-
+    # Stockholm_1_0()  # ???
diff -r 477d829d3250 -r c9e29ac5d099 infernal.tar.gz
Binary file infernal.tar.gz has changed
diff -r 477d829d3250 -r c9e29ac5d099 macros.xml
--- a/macros.xml	Sat Nov 11 16:01:09 2017 -0500
+++ b/macros.xml	Thu Sep 23 19:38:58 2021 +0000
@@ -2,11 +2,17 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package">infernal</requirement>
-            <requirement type="package" version="1.1.2">infernal</requirement>
-            <requirement type="package" version="8.25">coreutils</requirement>
+            <requirement type="package" version="1.1.4">infernal</requirement>
+            <requirement type="package" version="8.32">coreutils</requirement>
         </requirements>
     </xml>
-    <token name="@VERSION@">1.1.2</token>
+    <token name="@TOOL_VERSION@">1.1.4</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">infernal</xref>
+        </xrefs>
+    </xml>
     <xml name="stdio">
         <stdio>
             <exit_code range="1:" />
diff -r 477d829d3250 -r c9e29ac5d099 repository_dependencies.xml
--- a/repository_dependencies.xml	Sat Nov 11 16:01:09 2017 -0500
+++ b/repository_dependencies.xml	Thu Sep 23 19:38:58 2021 +0000
@@ -1,4 +1,4 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <repositories description="This requires the datatype definitions for Multiple Sequence Alignment (MSA) formats (e.g. STOCKHOLM, SELEX, ClustalW).">
-    <repository changeset_revision="70227007b991" name="msa_datatypes" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-</repositories>
+    <repository name="msa_datatypes" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="70227007b991"/>
+</repositories>
\ No newline at end of file
diff -r 477d829d3250 -r c9e29ac5d099 test-data/cmsearch_result.tabular
--- a/test-data/cmsearch_result.tabular	Sat Nov 11 16:01:09 2017 -0500
+++ b/test-data/cmsearch_result.tabular	Thu Sep 23 19:38:58 2021 +0000
@@ -1,56 +1,56 @@
-NC_013790.1	-	tRNA5	-	cm	1	72	362026	361955	-	no	1	0.50	0.0	71.5	1.3e-18	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2585265	2585193	-	no	1	0.60	0.0	70.2	3.3e-18	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	762490	762562	+	no	1	0.67	0.0	68.8	9e-18	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2041704	2041632	-	no	1	0.67	0.0	68.8	9e-18	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2351254	2351181	-	no	1	0.62	0.0	67.4	2.5e-17	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	735136	735208	+	no	1	0.59	0.0	67.2	3e-17	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2186013	2185941	-	no	1	0.53	0.0	66.4	5.2e-17	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2350593	2350520	-	no	1	0.66	0.0	64.8	1.6e-16	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2585187	2585114	-	no	1	0.59	0.0	64.1	2.8e-16	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	662185	662259	+	no	1	0.61	0.0	62.5	9.1e-16	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	360887	360815	-	no	1	0.55	0.0	62.1	1.2e-15	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2350984	2350911	-	no	1	0.53	0.0	61.7	1.6e-15	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2186090	2186019	-	no	1	0.54	0.0	60.7	3.3e-15	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2680159	2680233	+	no	1	0.67	0.0	60.4	4.1e-15	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2749945	2749874	-	no	1	0.53	0.0	59.5	7.9e-15	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2749839	2749768	-	no	1	0.53	0.0	59.5	7.9e-15	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	361676	361604	-	no	1	0.51	0.0	59.2	9.8e-15	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2585073	2584999	-	no	1	0.60	0.0	59.2	1e-14	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2130422	2130349	-	no	1	0.59	0.0	59.1	1.1e-14	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	546056	545947	-	no	1	0.61	0.0	58.9	1.2e-14	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	361915	361844	-	no	1	0.42	0.0	57.3	3.9e-14	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	97724	97795	+	no	1	0.49	0.0	57.0	5.1e-14	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2350717	2350646	-	no	1	0.68	0.0	56.7	6.1e-14	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	1873887	1873815	-	no	1	0.64	0.0	56.3	8e-14	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	360730	360659	-	no	1	0.40	0.0	55.6	1.4e-13	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2680310	2680384	+	no	1	0.52	0.0	54.3	3.5e-13	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2664806	2664732	-	no	1	0.60	0.0	54.3	3.6e-13	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	361061	360989	-	no	1	0.41	0.0	54.3	3.6e-13	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2130335	2130262	-	no	1	0.55	0.0	53.3	7.5e-13	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2151672	2151745	+	no	1	0.65	0.0	53.3	7.6e-13	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	319297	319370	+	no	1	0.62	0.0	51.4	2.9e-12	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	361753	361679	-	no	1	0.55	0.0	51.1	3.7e-12	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	360983	360912	-	no	1	0.50	0.0	51.1	3.8e-12	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	361456	361383	-	no	1	0.50	0.0	50.5	5.9e-12	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	362798	362727	-	no	1	0.51	0.0	50.1	7.4e-12	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	917722	917793	+	no	1	0.61	0.0	49.9	8.7e-12	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2583869	2583798	-	no	1	0.51	0.0	49.7	1.1e-11	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	362324	362252	-	no	1	0.51	0.0	49.4	1.3e-11	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	360811	360740	-	no	1	0.42	0.0	49.3	1.3e-11	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	1160526	1160609	+	no	1	0.60	0.0	47.7	4.3e-11	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	362403	362331	-	no	1	0.49	0.0	46.6	9.8e-11	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2327124	2327042	-	no	1	0.63	0.0	46.5	1.1e-10	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	995344	995263	-	no	1	0.49	0.0	46.4	1.2e-10	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	256772	256696	-	no	1	0.57	0.0	45.5	2.3e-10	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2584830	2584758	-	no	1	0.64	0.0	45.3	2.5e-10	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2351071	2350997	-	no	1	0.59	0.0	44.1	6.1e-10	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	362552	362482	-	no	1	0.55	0.0	44.0	6.5e-10	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	1064775	1064858	+	no	1	0.63	0.0	41.2	5.2e-09	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	361222	361150	-	no	1	0.45	0.0	40.0	1.2e-08	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	361369	361297	-	no	1	0.60	0.0	40.0	1.2e-08	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	361596	361513	-	no	1	0.61	0.0	38.1	4.8e-08	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	1913310	1913227	-	no	1	0.64	0.0	35.5	3.2e-07	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	363464	363381	-	no	1	0.51	0.0	32.7	2.6e-06	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	2584954	2584872	-	no	1	0.58	0.0	32.5	3e-06	!	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	363803	363716	-	no	1	0.50	0.0	20.0	0.027	?	Methanobrevibacter ruminantium M1 chromosome, complete genome
-NC_013790.1	-	tRNA5	-	cm	1	72	984373	984304	-	no	1	0.53	0.0	13.4	3.4	?	Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 362026 361955 - no 1 0.50 0.0 71.5 1.3e-18 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2585265 2585193 - no 1 0.60 0.0 70.2 3.3e-18 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 762490 762562 + no 1 0.67 0.0 68.8 9e-18 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2041704 2041632 - no 1 0.67 0.0 68.8 9e-18 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2351254 2351181 - no 1 0.62 0.0 67.4 2.5e-17 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 735136 735208 + no 1 0.59 0.0 67.2 3e-17 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2186013 2185941 - no 1 0.53 0.0 66.4 5.2e-17 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2350593 2350520 - no 1 0.66 0.0 64.8 1.6e-16 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2585187 2585114 - no 1 0.59 0.0 64.1 2.8e-16 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 662185 662259 + no 1 0.61 0.0 62.5 9.1e-16 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 360887 360815 - no 1 0.55 0.0 62.1 1.2e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2350984 2350911 - no 1 0.53 0.0 61.7 1.6e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2186090 2186019 - no 1 0.54 0.0 60.7 3.3e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2680159 2680233 + no 1 0.67 0.0 60.4 4.1e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2749945 2749874 - no 1 0.53 0.0 59.5 7.9e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2749839 2749768 - no 1 0.53 0.0 59.5 7.9e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 361676 361604 - no 1 0.51 0.0 59.2 9.8e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2585073 2584999 - no 1 0.60 0.0 59.2 1e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2130422 2130349 - no 1 0.59 0.0 59.1 1.1e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 546056 545947 - no 1 0.61 0.0 58.9 1.2e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 361915 361844 - no 1 0.42 0.0 57.3 3.9e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 97724 97795 + no 1 0.49 0.0 57.0 5.1e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2350717 2350646 - no 1 0.68 0.0 56.7 6.1e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 1873887 1873815 - no 1 0.64 0.0 56.3 8e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 360730 360659 - no 1 0.40 0.0 55.6 1.4e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2680310 2680384 + no 1 0.52 0.0 54.3 3.5e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2664806 2664732 - no 1 0.60 0.0 54.3 3.6e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 361061 360989 - no 1 0.41 0.0 54.3 3.6e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2130335 2130262 - no 1 0.55 0.0 53.3 7.5e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2151672 2151745 + no 1 0.65 0.0 53.3 7.6e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 319297 319370 + no 1 0.62 0.0 51.4 2.9e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 361753 361679 - no 1 0.55 0.0 51.1 3.7e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 360983 360912 - no 1 0.50 0.0 51.1 3.8e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 361456 361383 - no 1 0.50 0.0 50.5 5.9e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 362798 362727 - no 1 0.51 0.0 50.1 7.4e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 917722 917793 + no 1 0.61 0.0 49.9 8.7e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2583869 2583798 - no 1 0.51 0.0 49.7 1.1e-11 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 362324 362252 - no 1 0.51 0.0 49.4 1.3e-11 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 360811 360740 - no 1 0.42 0.0 49.3 1.3e-11 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 1160526 1160609 + no 1 0.60 0.0 47.7 4.3e-11 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 362403 362331 - no 1 0.49 0.0 46.6 9.8e-11 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2327124 2327042 - no 1 0.63 0.0 46.5 1.1e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 995344 995263 - no 1 0.49 0.0 46.4 1.2e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 256772 256696 - no 1 0.57 0.0 45.5 2.3e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2584830 2584758 - no 1 0.64 0.0 45.3 2.5e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2351071 2350997 - no 1 0.59 0.0 44.1 6.1e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 362552 362482 - no 1 0.55 0.0 44.0 6.5e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 1064775 1064858 + no 1 0.63 0.0 41.2 5.2e-09 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 361222 361150 - no 1 0.45 0.0 40.0 1.2e-08 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 361369 361297 - no 1 0.60 0.0 40.0 1.2e-08 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 361596 361513 - no 1 0.61 0.0 38.1 4.8e-08 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 1913310 1913227 - no 1 0.64 0.0 35.5 3.2e-07 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 363464 363381 - no 1 0.51 0.0 32.7 2.6e-06 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 2584954 2584872 - no 1 0.58 0.0 32.5 3e-06 ! Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 363803 363716 - no 1 0.50 0.0 20.0 0.027 ? Methanobrevibacter ruminantium M1 chromosome, complete genome
+NC_013790.1 - tRNA5 - cm 1 72 984373 984304 - no 1 0.53 0.0 13.4 3.4 ? Methanobrevibacter ruminantium M1 chromosome, complete genome
diff -r 477d829d3250 -r c9e29ac5d099 test-data/test_cmscan.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_cmscan.tabular	Thu Sep 23 19:38:58 2021 +0000
@@ -0,0 +1,15 @@
+#target	name	accession	query name	accession	mdl	mdl from	mdl to	seq from	seq to	strand	trunc	pass	gc	bias	score	E-value	inc	description of target
+5S_rRNA	RF00001	AAGA01015927.1	-	cm	1	119	59	174	+	no	1	0.66	0.0	77.3	3.3e-19	!	                 5S ribosomal RNA
+tRNA5	-	AAGA01015927.1	-	cm	1	72	229	302	+	no	1	0.62	0.0	62.4	9.3e-19	!	                 -
+tRNA5	-	AAGA01015927.1	-	cm	1	72	314	386	+	no	1	0.59	0.0	53.5	6e-16	!	                 -
+Cobalamin	RF00174	AAFY01022046.1	-	cm	32	191	934	832	-	5'	2	0.48	0.0	30.0	6.1e-09	!	                 Cobalamin riboswitch
+#																	                
+#	Program:	cmscan															                
+#	Version:	1.1.4	(Dec	2020)													                
+#	Pipeline	mode:	SCAN														                
+#	Query	file:	/tmp/tmp6jwp47cs/files/a/6/f/dataset_a6fe922b-72aa-4753-b4dd-cd3c716a4ae5.dat														                
+#	Target	file:	cmdb.cm														                
+#	Option	settings:	cmscan	-o	/dev/null	--tblout	$temp_tabular_output	--default	--cpu	1	cmdb.cm	/tmp/tmp6jwp47cs/files/a/6/f/dataset_a6fe922b-72aa-4753-b4dd-cd3c716a4ae5.dat					                
+#	Current	dir:	/tmp/tmp6jwp47cs/job_working_directory/000/13/working														                
+#	Date:	Thu	Sep	23	15:21:39	2021											                
+#	[ok]