# HG changeset patch
# User iuc
# Date 1534508569 14400
# Node ID 4ec6717872b1b415a6223f51a6f4d42d91409d57
# Parent  32e1bfc6b7b2faf81aebefd178a0c672c9f6a5fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a

diff -r 32e1bfc6b7b2 -r 4ec6717872b1 scpipe.xml
--- a/scpipe.xml	Wed Aug 15 13:54:40 2018 -0400
+++ b/scpipe.xml	Fri Aug 17 08:22:49 2018 -0400
@@ -28,7 +28,7 @@
     #set $fasta_name = re.sub('[^\w\-\s]', '_', str($ref_fasta.ref_fa_hist.element_identifier))
     ln -s '$ref_fasta.ref_fa_hist' '$fasta_name' &&
 #else:
-    #set $fasta_name = re.sub('[^\w\-\s]', '_', str($ref_fasta.ref_fa_builtin.element_identifier))
+    #set $fasta_name = os.path.basename(str($ref_fasta.ref_fa_builtin.fields.path))
     ln -s '$ref_fasta.ref_fa_builtin.fields.path' '$fasta_name' &&
 #end if
 
@@ -156,12 +156,12 @@
             help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No">
         </param>
         <section name="adv" title="Advanced Options">
-            <param argument="--rmlow" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with N in barcode or UMI. Default: Yes" />
-            <param argument="--rmN" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with low quality. Default: Yes" />
-            <param argument="--minq" type="integer" min="0" value="20" label="Minimum read quality. Default: 20" />
-            <param argument="--numbq" type="integer" min="0" value="2" label="Maximum number of bases below minq. Default: 2" />
-            <param argument="--stnd" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Perform strand-specific mapping. Default: Yes" />
-            <param argument="--max_mis" type="integer" min="0" value="1" label="Maximum mismatch allowed in barcode. Default: 1" />
+            <param argument="--rmlow" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with N in barcode or UMI" help="Default: Yes" />
+            <param argument="--rmN" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with low quality" help="Default: Yes" />
+            <param argument="--minq" type="integer" min="0" value="20" label="Minimum read quality" help="Default: 20" />
+            <param argument="--numbq" type="integer" min="0" value="2" label="Maximum number of bases below minq" help="Default: 2" />
+            <param argument="--stnd" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Perform strand-specific mapping" help="Default: Yes" />
+            <param argument="--max_mis" type="integer" min="0" value="1" label="Maximum mismatch allowed in barcode" help="Default: 1" />
             <param argument="--UMI_cor" type="integer" min="0" value="1" label="Correct UMI sequence error" help="0 means no correction, 1 means simple correction and merge UMI with distance 1. Default: 1" />
             <param argument="--gene_fl" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Remove low abundant genes" help="Low abundant is defined as only one copy of one UMI for this gene. Default: No" />
             <param argument="--max_reads" type="integer" min="0" value="1000000" label="Maximum reads processed" help="Maximum reads processed if detecting barcodes. Default: 1,000,000" />
@@ -206,6 +206,23 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Ensure built-in fasta works -->
+        <test>
+            <param name="fasta_source" value="cached"/>
+            <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/>
+            <param name="paired_format_selector" value="paired" />
+            <param name="in1" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R1.gz"/>
+            <param name="in2" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R2.gz"/>
+            <param name="us" value="-1"/>
+            <param name="max_reads" value="5000000"/>
+            <param name="min_count" value="100"/>
+            <param name="report" value="False" />
+            <output name="out_matrix" >
+                <assert_contents>
+                    <has_text text="ENSMUSG00000064351" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark
diff -r 32e1bfc6b7b2 -r 4ec6717872b1 test-data/cached_locally/all_fasta.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/all_fasta.loc	Fri Aug 17 08:22:49 2018 -0400
@@ -0,0 +1,1 @@
+mm10	mm10	mm10_Fasta	${__HERE__}/mm10_MT.fa
diff -r 32e1bfc6b7b2 -r 4ec6717872b1 test-data/cached_locally/mm10_MT.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/mm10_MT.fa	Fri Aug 17 08:22:49 2018 -0400
@@ -0,0 +1,100 @@
+>MT
+GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCC
+CATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCA
+AACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTA
+TCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCA
+GTGATAAATATTAAGCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAA
+ATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAA
+CGTGTCAACTATAAATAAATAAATAGAATTAAAATCCAACTTATATGTGAAAATTCATTG
+TTAGGACCTAAACTCAATAACGAAAGTAATTCTAGTCATTTATAATACACGACAGCTAAG
+ACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTA
+ACAAAACTATTTGCCAGAGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTA
+CTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCAT
+CTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGT
+AAGCAAAAGAATCAAACATAAAAACGTTAGGTCAAGGTGTAGCCAATGAAATGGGAAGAA
+ATGGGCTACATTTTCTTATAAAAGAACATTACTATACCCTTTATGAAACTAAAGGACTAA
+GGAGGATTTAGTAGTAAATTAAGAATAGAGAGCTTAATTGAATTGAGCAATGAAGTACGC
+ACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACA
+TCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAA
+TAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCA
+ATGAACACTCTGAACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATAT
+AAATCAAAACATTTATCCTACTAAAAGTATTGGAGAAAGAAATTCGTACATCTAGGAGCT
+ATAGAACTAGTACCGCAAGGGAAAGATGAAAGACTAATTAAAAGTAAGAACAAGCAAAGA
+TTAAACCTTGTACCTTTTGCATAATGAACTAACTAGAAAACTTCTAACTAAAAGAATTAC
+AGCTAGAAACCCCGAAACCAAACGAGCTACCTAAAAACAATTTTATGAATCAACTCGTCT
+ATGTGGCAAAATAGTGAGAAGATTTTTAGGTAGAGGTGAAAAGCCTAACGAGCTTGGTGA
+TAGCTGGTTACCCAAAAAATGAATTTAAGTTCAATTTTAAACTTGCTAAAAAAACAACAA
+AATCAAAAAGTAAGTTTAGATTATAGCCAAAAGAGGGACAGCTCTTCTGGAACGGAAAAA
+ACCTTTAATAGTGAATAATTAACAAAACAGCTTTTAACCATTGTAGGCCTAAAAGCAGCC
+ACCAATAAAGAAAGCGTTCAAGCTCAACATAAAATTTCAATTAATTCCATAATTTACACC
+AACTTCCTAAACTTAAAATTGGGTTAATCTATAACTTTATAGATGCAACACTGTTAGTAT
+GAGTAACAAGAATTCCAATTCTCCAGGCATACGCGTATAACAACTCGGATAACCATTGTT
+AGTTAATCAGACTATAGGCAATAATCACACTATAAATAATCCACCTATAACTTCTCTGTT
+AACCCAACACCGGAATGCCTAAAGGAAAGATCCAAAAAGATAAAAGGAACTCGGCAAACA
+AGAACCCCGCCTGTTTACCAAAAACATCACCTCTAGCATTACAAGTATTAGAGGCACTGC
+CTGCCCAGTGACTAAAGTTTAACGGCCGCGGTATCCTGACCGTGCAAAGGTAGCATAATC
+ACTTGTTCCTTAATTAGGGACTAGCATGAACGGCTAAACGAGGGTCCAACTGTCTCTTAT
+CTTTAATCAGTGAAATTGACCTTTCAGTGAAGAGGCTGAAATATAATAATAAGACGAGAA
+GACCCTATGGAGCTTAAATTATATAACTTATCTATTTAATTTATTAAACCTAATGGCCCA
+AAAACTATAGTATAAGTTTGAAATTTCGGTTGGGGTGACCTCGGAGAATAAAAAATCCTC
+CGAATGATTATAACCTAGACTTACAAGTCAAAGTAAAATCAACATATCTTATTGACCCAG
+ATATATTTTGATCAACGGACCAAGTTACCCTAGGGATAACAGCGCAATCCTATTTAAGAG
+TTCATATCGACAATTAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCAATGGTGTA
+GAAGCTATTAATGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACC
+GGAGCAATCCAGGTCGGTTTCTATCTATTTACGATTTCTCCCAGTACGAAAGGACAAGAG
+AAATAGAGCCACCTTACAAATAAGCGCTCTCAACTTAATTTATGAATAAAATCTAAATAA
+AATATATACGTACACCCTCTAACCTAGAGAAGGTTATTAGGGTGGCAGAGCCAGGAAATT
+GCGTAAGACTTAAAACCTTGTTCCCAGAGGTTCAAATCCTCTCCCTAATAGTGTTCTTTA
+TTAATATCCTAACACTCCTCGTCCCCATTCTAATCGCCATAGCCTTCCTAACATTAGTAG
+AACGCAAAATCTTAGGGTACATACAACTACGAAAAGGCCCTAACATTGTTGGTCCATACG
+GCATTTTACAACCATTTGCAGACGCCATAAAATTATTTATAAAAGAACCAATACGCCCTT
+TAACAACCTCTATATCCTTATTTATTATTGCACCTACCCTATCACTCACACTAGCATTAA
+GTCTATGAGTTCCCCTACCAATACCACACCCATTAATTAATTTAAACCTAGGGATTTTAT
+TTATTTTAGCAACATCTAGCCTATCAGTTTACTCCATTCTATGATCAGGATGAGCCTCAA
+ACTCCAAATACTCACTATTCGGAGCTTTACGAGCCGTAGCCCAAACAATTTCATATGAAG
+TAACCATAGCTATTATCCTTTTATCAGTTCTATTAATAAATGGATCCTACTCTCTACAAA
+CACTTATTACAACCCAAGAACACATATGATTACTTCTGCCAGCCTGACCCATAGCCATAA
+TATGATTTATCTCAACCCTAGCAGAAACAAACCGGGCCCCCTTCGACCTGACAGAAGGAG
+AATCAGAATTAGTATCAGGGTTTAACGTAGAATACGCAGCCGGCCCATTCGCGTTATTCT
+TTATAGCAGAGTACACTAACATTATTCTAATAAACGCCCTAACAACTATTATCTTCCTAG
+GACCCCTATACTATATCAATTTACCAGAACTCTACTCAACTAACTTCATAATAGAAGCTC
+TACTACTATCATCAACATTCCTATGGATCCGAGCATCTTATCCACGCTTCCGTTACGATC
+AACTTATACATCTTCTATGAAAAAACTTTCTACCCCTAACACTAGCATTATGTATGTGAC
+ATATTTCTTTACCAATTTTTACAGCGGGAGTACCACCATACATATAGAAATATGTCTGAT
+AAAAGAATTACTTTGATAGAGTAAATTATAGAGGTTCAAGCCCTCTTATTTCTAGGACAA
+TAGGAATTGAACCTACACTTAAGAATTCAAAATTCTCCGTGCTACCTAAACACCTTATCC
+TAATAGTAAGGTCAGCTAATTAAGCTATCGGGCCCATACCCCGAAAACGTTGGTTTAAAT
+CCTTCCCGTACTAATAAATCCTATCACCCTTGCCATCATCTACTTCACAATCTTCTTAGG
+TCCTGTAATCACAATATCCAGCACCAACCTAATACTAATATGAGTAGGCCTGGAATTCAG
+CCTACTAGCAATTATCCCCATACTAATCAACAAAAAAAACCCACGATCAACTGAAGCAGC
+AACAAAATACTTCGTCACACAAGCAACAGCCTCAATAATTATCCTCCTGGCCATCGTACT
+CAACTATAAACAACTAGGAACATGAATATTTCAACAACAAACAAACGGTCTTATCCTTAA
+CATAACATTAATAGCCCTATCCATAAAACTAGGCCTCGCCCCATTCCACTTCTGATTACC
+AGAAGTAACTCAAGGGATCCCACTGCACATAGGACTTATTCTTCTTACATGACAAAAAAT
+TGCTCCCCTATCAATTTTAATTCAAATTTACCCGCTACTCAACTCTACTATCATTTTAAT
+ACTAGCAATTACTTCTATTTTCATAGGGGCATGAGGAGGACTTAACCAAACACAAATACG
+AAAAATTATAGCCTATTCATCAATTGCCCACATAGGATGAATATTAGCAATTCTTCCTTA
+CAACCCATCCCTCACTCTACTCAACCTCATAATCTATATTATTCTTACAGCCCCTATATT
+CATAGCACTTATACTAAATAACTCTATAACCATCAACTCAATCTCACTTCTATGAAATAA
+AACTCCAGCAATACTAACTATAATCTCACTGATATTACTATCCCTAGGAGGCCTTCCACC
+ACTAACAGGATTCTTACCAAAATGAATTATCATCACAGAACTTATAAAAAACAACTGTCT
+AATTATAGCAACACTCATAGCAATAATAGCTCTACTAAACCTATTCTTTTATACTCGCCT
+AATTTATTCCACTTCACTAACAATATTTCCAACCAACAATAACTCAAAAATAATAACTCA
+CCAAACAAAAACTAAACCCAACCTAATATTTTCCACCCTAGCTATCATAAGCACAATAAC
+CCTACCCCTAGCCCCCCAACTAATTACCTAGAAGTTTAGGATATACTAGTCCGCGAGCCT
+TCAAAGCCCTAAGAAAACACACAAGTTTAACTTCTGATAAGGACTGTAAGACTTCATCCT
+ACATCTATTGAATGCAAATCAATTGCTTTAATTAAGCTAAGACCTCAACTAGATTGGCAG
+GAATTAAACCTACGAAAATTTAGTTAACAGCTAAATACCCTATTACTGGCTTCAATCTAC
+TTCTACCGCCGAAAAAAAAAAATGGCGGTAGAAGTCTTAGTAGAGATTTCTCTACACCTT
+CGAATTTGCAATTCGACATGAATATCACCTTAAGACCTCTGGTAAAAAGAGGATTTAAAC
+CTCTGTGTTTAGATTTACAGTCTAATGCTTACTCAGCCATTTTACCTATGTTCATTAATC
+GTTGATTATTCTCAACCAATCACAAAGATATCGGAACCCTCTATCTACTATTCGGAGCCT
+GAGCGGGAATAGTGGGTACTGCACTAAGTATTTTAATTCGAGCAGAATTAGGTCAACCAG
+GTGCACTTTTAGGAGATGACCAAATTTACAATGTTATCGTAACTGCCCATGCTTTTGTTA
+TAATTTTCTTCATAGTAATACCAATAATAATTGGAGGCTTTGGAAACTGACTTGTCCCAC
+TAATAATCGGAGCCCCAGATATAGCATTCCCACGAATAAATAATATAAGTTTTTGACTCC
+TACCACCATCATTTCTCCTTCTCCTAGCATCATCAATAGTAGAAGCAGGAGCAGGAACAG
+GATGAACAGTCTACCCACCTCTAGCCGGAAATCTAGCCCATGCAGGAGCATCAGTAGACC
+TAACAATTTTCTCCCTTCATTTAGCTGGAGTGTCATCTATTTTAGGTGCAATTAATTTTA
+TTACCACTATTATCAACATGAAACCCCCAGCCATAACACAGTATCAAACTCCACTATTTG
+TCTGATCCGTACTTATTACAGCCGTACTGCTCCTATTATCACTACCAGTGCTAGCCGCAG
diff -r 32e1bfc6b7b2 -r 4ec6717872b1 tool_data_table_conf.xml.test
--- a/tool_data_table_conf.xml.test	Wed Aug 15 13:54:40 2018 -0400
+++ b/tool_data_table_conf.xml.test	Fri Aug 17 08:22:49 2018 -0400
@@ -2,7 +2,7 @@
     <!-- Locations of genome fasta files -->
     <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
         <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/all_fasta.loc" />
+        <file path="${__HERE__}/test-data/cached_locally/all_fasta.loc" />
     </table>
 </tables>