Mercurial > repos > iuc > samtools_fixmate

annotate samtools_fixmate.xml @ 2:bc77b4b67147 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 16:01:34 +0000
parents 77af4d28aca3
children 24db20d85bfd
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bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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1 <tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@" profile="@PROFILE@">
0
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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2 <description>fill mate coordinates, ISIZE and mate related flags</description>
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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3 <macros>
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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4 <import>macros.xml</import>
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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5 </macros>
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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6 <expand macro="requirements"/>
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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7 <expand macro="stdio"/>
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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8 <expand macro="version_command"/>
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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9 <command><![CDATA[
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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10 @ADDTHREADS@
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bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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11 ## name sort input
0
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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12 #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'):
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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13 samtools sort
1
77af4d28aca3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
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14 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
2
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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15 -n
0
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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16 -O BAM
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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17 -o namesorted.bam
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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18 '$bamfile' &&
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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19 #else:
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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20 ln -s '$bamfile' namesorted.bam &&
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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21 #end if
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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22
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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23 samtools fixmate
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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24 -@ \$addthreads
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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25 $remsec
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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26 $noprop
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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27 $tempcigar
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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28 $addms
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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29 -O BAM
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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30 namesorted.bam
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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31 '$output'
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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32 ]]></command>
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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33 <inputs>
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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34 <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Select alignment" help="Set of aligned reads." />
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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35 <param name="remsec" type="boolean" argument="-r" truevalue="-r" falsevalue="" checked="false" label="Remove secondary and unmapped reads" />
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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36 <param name="noprop" type="boolean" argument="-p" truevalue="-p" falsevalue="" checked="false" label="Disable FR proper pair check" />
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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37 <param name="tempcigar" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Add template cigar ct tag" />
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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38 <param name="addms" type="boolean" argument="-m" truevalue="-m" falsevalue="" checked="false" label="Add ms (mate score) tags" help="These are used by markdup to select the best reads to keep." />
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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39 </inputs>
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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40 <outputs>
2
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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41 <!--<data name="output" format="sam" />-->
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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42 <data name="output" format="qname_sorted.bam"/>
0
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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43 </outputs>
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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44 <tests>
2
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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45 <!-- from https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2493-->
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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46 <!-- test_cmd($opts,out=>'fixmate/1_coord_sort.sam.expected', err=>'fixmate/1_coord_sort.sam.expected.err', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/1_coord_sort.sam -", expect_fail=>1);-->
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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47 <test>
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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48 <param name="bamfile" value="2_isize_overflow.sam" ftype="sam" />
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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49 <output name="output" file="2_isize_overflow.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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50 </test>
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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51 <!-- test_cmd($opts,out=>'fixmate/2_isize_overflow.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/2_isize_overflow.sam -");-->
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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52 <test>
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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53 <param name="bamfile" value="3_reverse_read_pp_lt.sam" ftype="sam" />
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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54 <output name="output" file="3_reverse_read_pp_lt.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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55 </test>
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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56 <!-- test_cmd($opts,out=>'fixmate/3_reverse_read_pp_lt.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/3_reverse_read_pp_lt.sam -");-->
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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57 <test>
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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58 <param name="bamfile" value="4_reverse_read_pp_equal.sam" ftype="sam" />
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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59 <output name="output" file="4_reverse_read_pp_equal.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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60 </test>
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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61 <!-- test_cmd($opts,out=>'fixmate/4_reverse_read_pp_equal.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/4_reverse_read_pp_equal.sam -");-->
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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62 <test>
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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63 <param name="bamfile" value="5_ct.sam" ftype="sam" />
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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64 <param name="tempcigar" value="-c" />
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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65 <output name="output" file="5_ct.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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66 </test>
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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67 <!-- test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");-->
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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68 <test>
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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69 <param name="bamfile" value="6_ct_replace.sam" ftype="sam" />
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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70 <param name="tempcigar" value="-c" />
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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71 <output name="output" file="6_ct_replace.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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72 </test>
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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73 <!-- test_cmd($opts,out=>'fixmate/6_ct_replace.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/6_ct_replace.sam -");-->
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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74 <test>
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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75 <param name="bamfile" value="7_two_read_mapped.sam" ftype="sam" />
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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76 <output name="output" file="7_two_read_mapped.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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77 </test>
bc77b4b67147 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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78 <!--test_cmd($opts,out=>'fixmate/7_two_read_mapped.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/7_two_read_mapped.sam -");-->
0
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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79 </tests>
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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80 <help>
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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81 **What it does**
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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82
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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83 Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment.
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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84 </help>
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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85 <expand macro="citations"/>
47c0cf039aae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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86 </tool>