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changeset 22:ae618321f34a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 12bd91ad0bc0a6471f34d1dd342c943f222a17d2
author iuc
date Mon, 30 Jan 2023 12:01:28 +0000
parents 914cfcba0ec8
children 8eb8750070d4
files macros.xml stringtie.xml stringtie_merge.xml test-data/stringtie_out1.gtf test-data/stringtie_out10.gtf test-data/stringtie_out11.gtf test-data/stringtie_out12.gtf test-data/stringtie_out1_re.gtf test-data/stringtie_out2.gtf test-data/stringtie_out2_re.gtf test-data/stringtie_out3.gtf test-data/stringtie_out3_re.gtf test-data/stringtie_out4.gtf test-data/stringtie_out4_re.gtf test-data/stringtie_out5.gtf test-data/stringtie_out6.gtf test-data/stringtie_out8.gtf test-data/stringtie_out9.gtf
diffstat 18 files changed, 36 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon Oct 31 20:08:02 2022 +0000
+++ b/macros.xml	Mon Jan 30 12:01:28 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.2.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="requirements">
         <requirements>
         <requirement type="package" version="@TOOL_VERSION@">stringtie</requirement>
--- a/stringtie.xml	Mon Oct 31 20:08:02 2022 +0000
+++ b/stringtie.xml	Mon Jan 30 12:01:28 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="stringtie" name="StringTie" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="stringtie" name="StringTie" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <description>transcript assembly and quantification</description>
     <xrefs>
         <xref type="bio.tools">stringtie</xref>
@@ -221,13 +221,13 @@
                     <valid initial="string.letters,string.digits"></valid>
                 </sanitizer>
             </param>
-            <param name="fraction" argument="-f" type="float" min="0.0" max="1.0" value="0.15" label="Minimum isoform fraction" help="Sets the minimum isoform abundance of the predicted transcripts as a fraction of the most abundant transcript assembled at a given locus. Lower abundance transcripts are often artifacts of incompletely spliced precursors of processed transcripts. Default: 0.15"/>
+            <param name="fraction" argument="-f" type="float" min="0.0" max="1.0" value="0.01" label="Minimum isoform fraction" help="Sets the minimum isoform abundance of the predicted transcripts as a fraction of the most abundant transcript assembled at a given locus. Lower abundance transcripts are often artifacts of incompletely spliced precursors of processed transcripts. Default: 0.05"/>
             <param name="min_tlen" argument="-m" type="integer" min="0" value="200" label="Minimum assembled transcript length" help="Sets the minimum length allowed for the predicted transcripts. Default: 200"/>
             <param name="min_anchor_len" argument="-a" type="integer" min="0" value="10" label="Minimum anchor length for junctions" help="Junctions that don't have spliced reads that align across them with at least this amount of bases on both sides are filtered out. Default: 10" />
             <param name="min_anchor_cov" argument="-j" type="integer" min="0" value="1" label="Minimum junction coverage" help="There should be at least this many spliced reads that align across a junction (i.e. junction coverage). This number can be fractional, since some reads align in more than one place. A read that aligns in n places will contribute 1/n to the junction coverage. Default: 1" />
-            <param name="min_bundle_cov" argument="-c" type="integer" min="0" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" help="Sets the minimum read coverage allowed for the predicted transcripts. A transcript with a lower coverage than this value is not shown in the output. Default: 2"/>
+            <param name="min_bundle_cov" argument="-c" type="integer" min="0" value="1" label="Minimum bundle reads per bp coverage to consider for assembly" help="Sets the minimum read coverage allowed for the predicted transcripts. A transcript with a lower coverage than this value is not shown in the output. Default: 2"/>
             <param name="bdist" argument="-g" type="integer" min="0" value="50" label="Gap between read mappings triggering a new bundle" help="Minimum locus gap separation value. Reads that are mapped closer than this distance are merged together in the same processing bundle. Default: 50 (bp)"/>
-            <param name="bundle_fraction" argument="-M" type="float" min="0.0" max="1.0" value="0.95" label="Fraction of bundle allowed to be covered by multi-hit reads"  help="Sets the maximum fraction of muliple-location-mapped reads that are allowed to be present at a given locus. Default: 0.95"/>
+            <param name="bundle_fraction" argument="-M" type="float" min="0.0" max="1.0" value="1" label="Fraction of bundle allowed to be covered by multi-hit reads"  help="Sets the maximum fraction of muliple-location-mapped reads that are allowed to be present at a given locus. Default: 0.95"/>
             <param name="disable_trimming" argument="-t" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Disable trimming of predicted transcripts based on coverage" help="This parameter disables trimming at the ends of the assembled transcripts. By default StringTie adjusts the predicted transcript's start and/or stop coordinates based on sudden drops in coverage of the assembled transcript. Default: No" />
             <param name="multi_mapping" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Disable multi-mapping correction" help="Default: No"/>
             <param name="point_features" type="data" format="tabular" optional="true" label="Input point-features dataset" help="Loads a list of point-features from a text feature file to guide the transcriptome assembly. Accepted point features are transcription start sites (TSS) and polyadenylation sites (CPAS). There are four tab-delimited columns in the feature file. The first three define the location of the point feature on the cromosome (sequence name, coordinate and strand), and the last is the type of the feature (TSS or CPAS)."/>
@@ -408,7 +408,7 @@
             <param name="use_guide" value="yes" />
             <param name="guide_gff_select" value="cached" />
             <param name="fraction" value="0.15" />
-            <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf"  compare="re_match" sort="true"/>
+            <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <!-- Test mixed reads input -->
         <test expect_num_outputs="1">
@@ -417,7 +417,13 @@
                 <param name="input_bam_short" ftype="bam" value="short_reads.bam" />
                 <param name="input_bam_long" ftype="bam" value="long_reads.bam" />
             </conditional>            
-            <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <output name="output_gtf" ftype="gtf">
+                <assert_contents>
+                    <has_text text="5.043160"/>
+                    <has_text text="StringTie version @TOOL_VERSION@"/>
+                    <has_n_lines n="87"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- Test cram input -->
         <test expect_num_outputs="1">
@@ -429,7 +435,7 @@
             <output name="output_gtf" ftype="gtf">
                 <assert_contents>
                     <has_text text="gi|251831106|ref|NC_012920.1|"/>
-                    <has_text text="StringTie version 2.2.1"/>
+                    <has_text text="StringTie version @TOOL_VERSION@"/>
                 </assert_contents>
             </output>
         </test>
--- a/stringtie_merge.xml	Mon Oct 31 20:08:02 2022 +0000
+++ b/stringtie_merge.xml	Mon Jan 30 12:01:28 2023 +0000
@@ -28,13 +28,13 @@
     <inputs>
         <param name="input_gtf" type="data" format="gtf,gff3" multiple="true" label="Transcripts" help="In GTF or GFF3 format" />
         <param name="guide_gff" argument="-G" type="data" format="gtf,gff3" optional="true" label="Reference annotation to include in the merging" />
-        <param name="min_len" argument="-m" type="integer" value="50" label="Minimum input transcript length to include in the merge" />
-        <param name="min_cov" argument="-c" type="integer" value="0" label="Minimum input transcript coverage to include in the merge" />
-        <param name="min_fpkm" argument="-F" type="float" value="1.0" label="Minimum input transcript FPKM to include in the merge" />
-        <param name="min_tpm" argument="-T" type="float" value="1.0" label="Minimum input transcript TPM to include in the merge" />
+        <param name="min_len" argument="-m" type="integer" min="0" value="50" label="Minimum input transcript length to include in the merge" />
+        <param name="min_cov" argument="-c" type="integer" min="0" value="0" label="Minimum input transcript coverage to include in the merge" />
+        <param name="min_fpkm" argument="-F" type="float" min="0" value="1" label="Minimum input transcript FPKM to include in the merge" />
+        <param name="min_tpm" argument="-T" type="float" min="0" value="1" label="Minimum input transcript TPM to include in the merge" />
         <param name="min_iso" argument="-f" type="float" value="0.01" label="Minimum isoform fraction" />
         <param name="gap_len" argument="-g" type="integer" value="250" label="Gap between transcripts to merge together" />
-        <param name="keep_introns" argument="-i" type="boolean" truevalue="-i" falsevalue="" label="Keep merged transcripts with retained introns" help="By default these are not kept unless there is strong evidence for them" />
+        <param name="keep_introns" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Keep merged transcripts with retained introns" help="By default these are not kept unless there is strong evidence for them" />
     </inputs>
     <outputs>
         <data name="out_gtf" format="gtf" />
@@ -43,12 +43,12 @@
         <test>
             <param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" />
             <param name="guide_gff" ftype="gtf" value="stringtie_in.gtf" />
-            <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" compare="re_match" sort="true" />
+            <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <test>
             <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
             <param name="guide_gff" ftype="gtf" value="stringtie_merge_in3.gtf" />
-            <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" compare="re_match" sort="true" />
+            <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
         <test>
             <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
--- a/test-data/stringtie_out1.gtf	Mon Oct 31 20:08:02 2022 +0000
+++ b/test-data/stringtie_out1.gtf	Mon Jan 30 12:01:28 2023 +0000
@@ -1,4 +1,4 @@
-# stringtie /tmp/tmpgqe071sy/files/8/a/5/dataset_8a57065f-d332-4a26-8aa0-9d511312d8a6.dat -o /tmp/tmpgqe071sy/files/b/4/6/dataset_b46e6244-1199-4c7b-946c-111d2b3c98c7.dat -p 1 -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
+# stringtie /tmp/tmpgqe071sy/files/8/a/5/dataset_8a57065f-d332-4a26-8aa0-9d511312d8a6.dat -o /tmp/tmpgqe071sy/files/b/4/6/dataset_b46e6244-1199-4c7b-946c-111d2b3c98c7.dat -p 1 -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
 # StringTie version 2.2.1
 test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "49.237373";
--- a/test-data/stringtie_out10.gtf	Mon Oct 31 20:08:02 2022 +0000
+++ b/test-data/stringtie_out10.gtf	Mon Jan 30 12:01:28 2023 +0000
@@ -1,5 +1,5 @@
 # StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -L -E 25 -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+# stringtie /[-_/a-zA-Z0-9]+\.dat -L -E 25 -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "54\.160000";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
 test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.777779";
--- a/test-data/stringtie_out11.gtf	Mon Oct 31 20:08:02 2022 +0000
+++ b/test-data/stringtie_out11.gtf	Mon Jan 30 12:01:28 2023 +0000
@@ -1,5 +1,5 @@
 # StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -L -E 30 -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+# stringtie /[-_/a-zA-Z0-9]+\.dat -L -E 30 -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
 chr19\tStringTie\texon\t567221\t567648\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.815421";
 chr19\tStringTie\texon\t571310\t571579\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "4\.559259";
 chr19\tStringTie\texon\t571440\t571596\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.859873";
--- a/test-data/stringtie_out12.gtf	Mon Oct 31 20:08:02 2022 +0000
+++ b/test-data/stringtie_out12.gtf	Mon Jan 30 12:01:28 2023 +0000
@@ -1,5 +1,5 @@
 # StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat -E 25 -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+# stringtie /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat -E 25 -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
 chr16\tStringTie\texon\t784986\t786377\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "1"; cov "33\.698273";
 chr16\tStringTie\texon\t786827\t786928\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "2"; cov "24\.970589";
 chr16\tStringTie\texon\t787077\t787179\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.[0-9+]"; exon_number "3"; cov "24\.747572";
--- a/test-data/stringtie_out1_re.gtf	Mon Oct 31 20:08:02 2022 +0000
+++ b/test-data/stringtie_out1_re.gtf	Mon Jan 30 12:01:28 2023 +0000
@@ -1,5 +1,5 @@
 # StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000";
 test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "49\.237373";
--- a/test-data/stringtie_out2.gtf	Mon Oct 31 20:08:02 2022 +0000
+++ b/test-data/stringtie_out2.gtf	Mon Jan 30 12:01:28 2023 +0000
@@ -1,4 +1,4 @@
-# stringtie /tmp/tmpgqe071sy/files/c/e/6/dataset_ce6d871e-dc50-4710-8c21-385b1a4fcd2e.dat -o /tmp/tmpgqe071sy/files/e/8/2/dataset_e82c3d81-e413-4566-a538-1ef066ef2348.dat -p 1 -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
+# stringtie /tmp/tmpgqe071sy/files/c/e/6/dataset_ce6d871e-dc50-4710-8c21-385b1a4fcd2e.dat -o /tmp/tmpgqe071sy/files/e/8/2/dataset_e82c3d81-e413-4566-a538-1ef066ef2348.dat -p 1 -f 0.17 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
 # StringTie version 2.2.1
 test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "49.237373";
--- a/test-data/stringtie_out2_re.gtf	Mon Oct 31 20:08:02 2022 +0000
+++ b/test-data/stringtie_out2_re.gtf	Mon Jan 30 12:01:28 2023 +0000
@@ -1,5 +1,5 @@
 # StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.17 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000";
 test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "49\.237373";
--- a/test-data/stringtie_out3.gtf	Mon Oct 31 20:08:02 2022 +0000
+++ b/test-data/stringtie_out3.gtf	Mon Jan 30 12:01:28 2023 +0000
@@ -1,4 +1,4 @@
-# stringtie /tmp/tmpgqe071sy/files/8/6/e/dataset_86e4ed94-6458-4fd6-b8ae-dc5f7acd75ac.dat -o /tmp/tmpgqe071sy/files/5/7/7/dataset_57773891-c25a-4102-a817-04fa6e876cf3.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95
+# stringtie /tmp/tmpgqe071sy/files/8/6/e/dataset_86e4ed94-6458-4fd6-b8ae-dc5f7acd75ac.dat -o /tmp/tmpgqe071sy/files/5/7/7/dataset_57773891-c25a-4102-a817-04fa6e876cf3.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
 # StringTie version 2.2.1
 test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373";
--- a/test-data/stringtie_out3_re.gtf	Mon Oct 31 20:08:02 2022 +0000
+++ b/test-data/stringtie_out3_re.gtf	Mon Jan 30 12:01:28 2023 +0000
@@ -1,5 +1,5 @@
 # StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
 test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373";
--- a/test-data/stringtie_out4.gtf	Mon Oct 31 20:08:02 2022 +0000
+++ b/test-data/stringtie_out4.gtf	Mon Jan 30 12:01:28 2023 +0000
@@ -1,4 +1,4 @@
-# stringtie /tmp/tmpgqe071sy/files/5/8/5/dataset_5851f244-d011-47e4-b6ac-bb6119b6497b.dat -o /tmp/tmpgqe071sy/files/d/a/6/dataset_da695139-3493-41cc-9409-8085cad59f40.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -A /tmp/tmpgqe071sy/files/8/7/d/dataset_87d1ffdf-8041-4fc6-b9d7-7cd794f69cd8.dat
+# stringtie /tmp/tmpgqe071sy/files/5/8/5/dataset_5851f244-d011-47e4-b6ac-bb6119b6497b.dat -o /tmp/tmpgqe071sy/files/d/a/6/dataset_da695139-3493-41cc-9409-8085cad59f40.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.17 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1 -A /tmp/tmpgqe071sy/files/8/7/d/dataset_87d1ffdf-8041-4fc6-b9d7-7cd794f69cd8.dat
 # StringTie version 2.2.1
 test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
 test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373";
--- a/test-data/stringtie_out4_re.gtf	Mon Oct 31 20:08:02 2022 +0000
+++ b/test-data/stringtie_out4_re.gtf	Mon Jan 30 12:01:28 2023 +0000
@@ -1,5 +1,5 @@
 # StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95( -A /[-_/a-zA-Z0-9]+\.dat)?
+# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.17 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0( -A /[-_/a-zA-Z0-9]+\.dat)?
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
 test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373";
--- a/test-data/stringtie_out5.gtf	Mon Oct 31 20:08:02 2022 +0000
+++ b/test-data/stringtie_out5.gtf	Mon Jan 30 12:01:28 2023 +0000
@@ -1,5 +1,5 @@
 # StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -C /[-_/a-zA-Z0-9]+\.dat -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -C /[-_/a-zA-Z0-9]+\.dat -b \./special_de_output/sample1/ -f 0\.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
 test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373";
--- a/test-data/stringtie_out6.gtf	Mon Oct 31 20:08:02 2022 +0000
+++ b/test-data/stringtie_out6.gtf	Mon Jan 30 12:01:28 2023 +0000
@@ -1,5 +1,5 @@
 # StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -C /[-_/a-zA-Z0-9]+\.dat -e -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -C /[-_/a-zA-Z0-9]+\.dat -e -b \./special_de_output/sample1/ -f 0\.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000";
 test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "49\.237373";
--- a/test-data/stringtie_out8.gtf	Mon Oct 31 20:08:02 2022 +0000
+++ b/test-data/stringtie_out8.gtf	Mon Jan 30 12:01:28 2023 +0000
@@ -1,5 +1,5 @@
 # StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
 test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373";
--- a/test-data/stringtie_out9.gtf	Mon Oct 31 20:08:02 2022 +0000
+++ b/test-data/stringtie_out9.gtf	Mon Jan 30 12:01:28 2023 +0000
@@ -1,5 +1,5 @@
 # StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95
+# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
 test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
 test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
 test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373";