Mercurial > repos > iuc > samtools_fastx

annotate samtools_fastx.xml @ 3:b3d99709fe1a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 5cb103832529f17e5c72e7f122758c13519fbe5e
author iuc
date Mon, 15 Aug 2022 09:16:56 +0000
parents 720217c23995
children 66e23b11feae
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
b3d99709fe1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 5cb103832529f17e5c72e7f122758c13519fbe5e
iuc
parents: 2
diff changeset
1 <tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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2 <description>extract FASTA or FASTQ from alignment files</description>
0
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
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3 <macros>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
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4 <import>macros.xml</import>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
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5 </macros>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
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6 <expand macro="requirements" />
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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7 <expand macro="stdio"/>
0
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
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8 <expand macro="version_command" />
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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9 <command><![CDATA[
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
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10 @ADDTHREADS@
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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11 ## name sort input file if neccessary
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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12 #if not $input.is_of_type('qname_sorted.bam', 'qname_input_sorted.bam'):
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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13 samtools sort -@ \$addthreads -n '$input' -T "\${TMPDIR:-.}" > input &&
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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14 #else:
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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15 ln -s '$input' input &&
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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16 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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17
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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18 #set command=str($output_fmt_cond.output_fmt_select)[:5]
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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19
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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20 samtools $command
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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21 #if str($output_fmt_cond.output_fmt_select).startswith('fastq'):
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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22 #if str($output_fmt_cond.default_quality) != '':
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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23 -v $output_fmt_cond.default_quality
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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24 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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25 $output_fmt_cond.output_quality
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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26 $output_fmt_cond.ilumina_casava
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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27 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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28 $copy_tags
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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29 #if str($copy_arb_tags) != '':
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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30 -T '$copy_arb_tags'
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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31 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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32 $read_numbering
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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33 #if 'r0' in str($outputs):
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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34 -0 nonspecific.$output_fmt_cond.output_fmt_select
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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35 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
36 #if 'r1' in str($outputs):
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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37 -1 forward.$output_fmt_cond.output_fmt_select
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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38 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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39 #if 'r2' in str($outputs):
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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40 -2 reverse.$output_fmt_cond.output_fmt_select
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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41 #end if
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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42 #set $filter = $inclusive_filter
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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43 @FLAGS@
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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44 -f $flags
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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45 #set $filter = $exclusive_filter
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
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46 @FLAGS@
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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47 -F $flags
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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48 #set $filter = $exclusive_filter_all
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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49 @FLAGS@
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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50 -G $flags
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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51 #if 's' in str($outputs):
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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52 -s singletons.$output_fmt_cond.output_fmt_select
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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53 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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54 #if str($idxout_cond.idxout_select) == 'yes':
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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55 #if str($idxout_cond.write1st) == 'yes':
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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56 --i1 i1.$output_fmt_cond.output_fmt_select
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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57 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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58 #if str($idxout_cond.write2nd) == 'yes':
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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59 --i2 i2.$output_fmt_cond.output_fmt_select
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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60 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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61 #if str($idxout_cond.index_format) != '':
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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62 --index-format $idxout_cond.index_format
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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63 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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64 #if str($idxout_cond.barcode_tag) != '':
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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65 --barcode-tag $idxout_cond.barcode_tag
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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66 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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67 #if str($idxout_cond.quality_tag) != '':
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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68 --quality-tag $idxout_cond.quality_tag
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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69 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
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70 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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71
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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72 input
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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73
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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74 #if str($outputs)=='None' or 'other' in str($outputs):
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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75 ## since currently stdout in not zipped (samtools doesn't know about the extension)
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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76 #if str($output_fmt_cond.output_fmt_select).endswith('.gz'):
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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77 | gzip -
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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78 #end if
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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79 > output.$output_fmt_cond.output_fmt_select
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80 && ln -s output.$output_fmt_cond.output_fmt_select output
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81 #else
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82 ## otherwise the remaining sequences would show up in the datasets info box
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83 > /dev/null
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84 #end if
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85 #if 'r0' in str($outputs):
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86 && ln -s nonspecific.$output_fmt_cond.output_fmt_select nonspecific
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87 #end if
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88 #if 'r1' in str($outputs):
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89 && ln -s forward.$output_fmt_cond.output_fmt_select forward
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90 #end if
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91 #if 'r2' in str($outputs):
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92 && ln -s reverse.$output_fmt_cond.output_fmt_select reverse
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93 #end if
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94 #if 's' in str($outputs):
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95 && ln -s singletons.$output_fmt_cond.output_fmt_select singletons
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96 #end if
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97 #if str($idxout_cond.idxout_select) == 'yes':
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98 #if str($idxout_cond.write1st) == 'yes':
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99 && ln -s i1.$output_fmt_cond.output_fmt_select i1
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100 #end if
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101 #if str($idxout_cond.write2nd) == 'yes':
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102 && ln -s i2.$output_fmt_cond.output_fmt_select i2
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103 #end if
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104 #end if
0
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105 ]]>
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106 </command>
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107 <inputs>
1
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108 <param name="input" type="data" format="sam,bam,cram" label="BAM or SAM file to convert" />
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109 <conditional name="output_fmt_cond">
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110 <param name="output_fmt_select" type="select" label="Output format">
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111 <option value="fasta" selected="True">FASTA</option>
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112 <option value="fastqsanger">FASTQ</option>
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113 <option value="fasta.gz">compressed FASTA</option>
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114 <option value="fastqsanger.gz">compressed FASTQ</option>
0
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115 </param>
1
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116 <when value="fastqsanger">
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117 <param name="default_quality" argument="-v" type="integer" optional="True" label="Default quality if none is given" />
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118 <param name="output_quality" argument="-O" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Output quality in the OQ tag if available" />
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119 <param name="ilumina_casava" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)" />
0
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120 </when>
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121 <when value="fasta" />
1
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122 <when value="fastqsanger.gz">
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123 <param name="default_quality" argument="-v" type="integer" optional="True" label="Default quality if none is given" />
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124 <param name="output_quality" argument="-O" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Output quality in the OQ tag if available" />
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125 <param name="ilumina_casava" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)" />
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126 </when>
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127 <when value="fasta.gz" />
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128 </conditional>
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129 <param name="outputs" type="select" multiple="true" label="outputs">
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130 <option value="other" selected="true">others</option>
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131 <option value="r1">READ1</option>
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132 <option value="r2">READ2</option>
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133 <option value="s">singletons</option>
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134 <option value="r0">unspecific</option>
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135 <help>disjoint subsets of the reads can be redirected to separate data sets. "READ[12]" are reads for which the READ[12] flag is set and the READ[21] flag is not set. "unspecific" reads are those for which both ore neither of these flags are set. "singletons" are the singleto reads. Note that if selected READ1 and READ2 contain only the paired reads. "other" are the remaining reads. If onlz 'others' or nothing is selected all reads go to a single data set. </help>
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136 </param>
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137 <param name="copy_tags" argument="-t" type="boolean" truevalue="-t" falsevalue="" label="Copy RG/BC/QT tags to output header" />
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138 <param name="copy_arb_tags" argument="-T" type="text" optional="true" label="copy arbitrary tags to the FASTA header line" />
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139 <param name="read_numbering" type="select" label="Omit or append read numbers">
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140 <option value="" selected="True">no</option>
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141 <option value="-n">Do not append /1 and /2 to read names</option>
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142 <option value="-N">always append /1 and /2 to read name</option>
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143 </param>
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144 <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set">
2
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145 <expand macro="flag_options"/>
1
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146 </param>
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147 <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set">
2
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148 <expand macro="flag_options" s256="true" s2048="true"/>
1
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149 </param>
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150 <param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set">
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151 <expand macro="flag_options" />
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152 </param>
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153
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154 <conditional name="idxout_cond">
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155 <param name="idxout_select" type="select" label="Write index read files">
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156 <option value="no" selected="True">No</option>
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157 <option value="yes">Yes (beta: feedback welcome)</option>
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158 </param>
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159 <when value="no" />
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160 <when value="yes">
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161 <param name="write1st" argument="--i1" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="write first index reads to extra data set" />
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162 <param name="write2nd" argument="--i2" type="boolean" truevalue="yes" falsevalue="no" checked='true' label="write second index reads to extra data set" />
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163 <param name="index_format" argument="--index-format" type="text" label="Index format: How to parse barcode and quality tags">
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164 <help>
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165 The index-format string describes how to parse the barcode and quality tags, for example:
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166 i14i8 the first 14 characters are index 1, the next 8 characters are index 2
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167 n8i14 ignore the first 8 characters, and use the next 14 characters for index 1
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168 If the tag contains a separator, then the numeric part can be replaced with '*' to mean
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169 'read until the separator or end of tag', for example:
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170 n*i* ignore the left part of the tag until the separator, then use the second part
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171 of the tag as index 1
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172 </help>
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173 </param>
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174 <param name="barcode_tag" argument="--barcode-tag" type="text" optional="True" label="Barcode tag [default: BC]"/>
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175 <param name="quality_tag" argument="--quality-tag" type="text" optional="True" label="Quality tag [default: QT]"/>
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176 </when>
0
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177 </conditional>
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178 </inputs>
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179 <outputs>
1
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180 <data name="nonspecific" format="fasta" from_work_dir="nonspecific" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (nonspecific)">
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181 <filter>'r0' in str(outputs)</filter>
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182 <actions>
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183 <action type="format">
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184 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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185 </action>
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186 </actions>
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187 </data>
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188 <data name="forward" format="fasta" from_work_dir="forward" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (READ1)">
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189 <filter>'r1' in str(outputs)</filter>
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190 <actions>
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191 <action type="format">
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192 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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193 </action>
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194 </actions>
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195 </data>
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196 <data name="reverse" format="fasta" from_work_dir="reverse" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (READ2)">
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197 <filter>'r2' in str(outputs)</filter>
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198 <actions>
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199 <action type="format">
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200 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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201 </action>
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202 </actions>
0
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203 </data>
1
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204 <data name="singletons" format="fasta" from_work_dir="singletons" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (singletons)">
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205 <filter>'s' in str(outputs)</filter>
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206 <actions>
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207 <action type="format">
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208 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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209 </action>
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210 </actions>
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211 </data>
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212 <data name="output" format="fasta" from_work_dir="output" label="${on_string} converted to ${output_fmt_cond.output_fmt_select}">
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213 <filter>str(outputs)=='None' or 'other' in str(outputs)</filter>
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214 <actions>
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215 <action type="format">
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216 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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217 </action>
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218 </actions>
0
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219 </data>
1
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220 <data name="i1" format="fasta" from_work_dir="i1" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (1st index)">
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221 <filter>idxout_cond['idxout_select']=='yes' and idxout_cond['write1st']</filter>
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222 <actions>
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223 <action type="format">
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224 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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225 </action>
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226 </actions>
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227 </data>
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228 <data name="i2" format="fasta" from_work_dir="i2" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (2nd index)">
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229 <filter>idxout_cond['idxout_select']=='yes' and idxout_cond['write2nd']</filter>
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230 <actions>
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231 <action type="format">
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232 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
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233 </action>
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234 </actions>
0
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235 </data>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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236 </outputs>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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237 <tests>
1
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238 <!-- tests from original Galaxy tool -->
0
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239 <test>
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240 <param name="input" value="samtools_fastx-in1.bam" ftype="bam" />
1
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241 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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242 <param name="output_fmt_select" value="fasta" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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243 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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244 <param name="outputs" value="other" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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245 <output name="output" file="samtools_fastx-out1.fasta" ftype="fasta" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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246 </test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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247 <test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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248 <param name="input" value="samtools_fastx-in2.bam" ftype="bam" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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249 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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250 <param name="output_fmt_select" value="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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251 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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252 <param name="outputs" value="r0,r1,r2" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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253 <output name="nonspecific" file="samtools_fastx-out2-1.fastq" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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254 <output name="forward" file="samtools_fastx-out2-2.fastq" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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255 <output name="reverse" file="samtools_fastx-out2-3.fastq" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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256 </test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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257 <test>
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258 <param name="input" value="samtools_fastx-in3.sam" ftype="sam" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
259 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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260 <param name="output_fmt_select" value="fasta" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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261 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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262 <param name="outputs" value="r0,r1,r2" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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263 <output name="nonspecific" file="samtools_fastx-out3-1.fasta" ftype="fasta" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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264 <output name="forward" file="samtools_fastx-out3-2.fasta" ftype="fasta" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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265 <output name="reverse" file="samtools_fastx-out3-3.fasta" ftype="fasta" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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266 </test>
2
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267 <!-- tests from original Galaxy tool with gz output. for some reason gzip (which is used
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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268 for compressing stdout does not give exactly the same file contents .. the other
1
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269 compressed files seem to)-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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270 <test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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271 <param name="input" value="samtools_fastx-in1.bam" ftype="bam" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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272 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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273 <param name="output_fmt_select" value="fasta.gz" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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274 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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275 <param name="outputs" value="other" />
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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276 <output name="output" file="samtools_fastx-out1.fasta.gz" ftype="fasta.gz" decompress="true"/>
0
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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277 </test>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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278 <test>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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279 <param name="input" value="samtools_fastx-in2.bam" ftype="bam" />
1
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280 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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281 <param name="output_fmt_select" value="fastqsanger.gz" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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282 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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283 <param name="outputs" value="r0,r1,r2" />
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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284 <output name="nonspecific" file="samtools_fastx-out2-1.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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285 <output name="forward" file="samtools_fastx-out2-2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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286 <output name="reverse" file="samtools_fastx-out2-3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
0
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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287 </test>
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288 <test>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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289 <param name="input" value="samtools_fastx-in3.sam" ftype="sam" />
1
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290 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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291 <param name="output_fmt_select" value="fasta.gz" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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292 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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293 <param name="outputs" value="r0,r1,r2" />
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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294 <output name="nonspecific" file="samtools_fastx-out3-1.fasta.gz" ftype="fasta.gz" decompress="true" />
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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295 <output name="forward" file="samtools_fastx-out3-2.fasta.gz" ftype="fasta.gz" decompress="true" />
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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296 <output name="reverse" file="samtools_fastx-out3-3.fasta.gz" ftype="fasta.gz" decompress="true" />
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
297 </test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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298 <!-- tests from: https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2313-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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299 <!--# basic 2 output test without singleton tracking-->
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300 <!--test_cmd($opts, out=>'bam2fq/1.stdout.expected', out_map=>{'1.fq' => 'bam2fq/1.1.fq.expected', '2.fq' => 'bam2fq/1.2.fq.expected'},cmd=>"$$opts{bin}/samtools fastq @$threads -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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301 <test>
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302 <param name="input" value="bam2fq.001.sam" ftype="sam" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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303 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
304 <param name="output_fmt_select" value="fastqsanger" />
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305 </conditional>
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306 <param name="outputs" value="r1,r2,other" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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307 <output name="forward" file="1.1.fq.expected" ftype="fastqsanger" />
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308 <output name="reverse" file="1.2.fq.expected" ftype="fastqsanger" />
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309 <output name="output" file="1.stdout.expected" ftype="fastqsanger" />
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310 </test>
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311 <!--# basic 2 output test with singleton tracking but no singleton-->
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312 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/2.1.fq.expected', '2.fq' => 'bam2fq/2.2.fq.expected', 's.fq' => 'bam2fq/2.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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313 <test>
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314 <param name="input" value="bam2fq.001.sam" ftype="sam" />
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315 <conditional name="output_fmt_cond">
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316 <param name="output_fmt_select" value="fastqsanger" />
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317 </conditional>
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318 <param name="outputs" value="r1,r2,s,other" />
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319 <output name="forward" file="2.1.fq.expected" ftype="fastqsanger" />
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320 <output name="reverse" file="2.2.fq.expected" ftype="fastqsanger" />
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321 <output name="singletons" file="2.s.fq.expected" ftype="fastqsanger" />
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322 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
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323 </test>
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324 <!--# basic 2 output test with singleton tracking with a singleton in the middle-->
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325 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/3.1.fq.expected', '2.fq' => 'bam2fq/3.2.fq.expected', 's.fq' => 'bam2fq/3.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.002.sam");-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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326 <test>
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327 <param name="input" value="bam2fq.002.sam" ftype="sam" />
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328 <conditional name="output_fmt_cond">
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329 <param name="output_fmt_select" value="fastqsanger" />
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330 </conditional>
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331 <param name="outputs" value="r1,r2,s,other" />
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332 <output name="forward" file="3.1.fq.expected" ftype="fastqsanger" />
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333 <output name="reverse" file="3.2.fq.expected" ftype="fastqsanger" />
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334 <output name="singletons" file="3.s.fq.expected" ftype="fastqsanger" />
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335 <output name="output" file="3.stdout.expected" ftype="fastqsanger" />
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336 </test>
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337 <!--# basic 2 output test with singleton tracking with a singleton as last read-->
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338 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.003.sam");-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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339 <test>
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340 <param name="input" value="bam2fq.003.sam" ftype="sam" />
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341 <conditional name="output_fmt_cond">
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342 <param name="output_fmt_select" value="fastqsanger" />
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343 </conditional>
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344 <param name="outputs" value="r1,r2,s,other" />
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345 <output name="forward" file="4.1.fq.expected" ftype="fastqsanger" />
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346 <output name="reverse" file="4.2.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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347 <output name="singletons" file="4.s.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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348 <output name="output" file="4.stdout.expected" ftype="fastqsanger" />
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349 </test>
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350 <!--# tag output test with singleton tracking with a singleton as last read-->
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351 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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352 <test>
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353 <param name="input" value="bam2fq.004.sam" ftype="sam" />
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354 <conditional name="output_fmt_cond">
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355 <param name="output_fmt_select" value="fastqsanger" />
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356 </conditional>
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357 <param name="outputs" value="r1,r2,s,other" />
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358 <conditional name="idxout_cond">
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359 <param name="idxout_select" value="yes"/>
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360 <param name="write1st" value="yes"/>
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361 <param name="barcode_tag" value="BC"/>
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362 <param name="index_format" value="n2i2"/>
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363 </conditional>
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364 <output name="forward" file="4.1.fq.expected" ftype="fastqsanger" />
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365 <output name="reverse" file="4.2.fq.expected" ftype="fastqsanger" />
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366 <output name="singletons" file="4.s.fq.expected" ftype="fastqsanger" />
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367 <output name="output" file="4.stdout.expected" ftype="fastqsanger" />
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368 <output name="i1" file="bc.fq.expected" ftype="fastqsanger" />
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369 </test>
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370 <!--# test -O flag with no OQ tags-->
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371 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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372 <test>
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373 <param name="input" value="bam2fq.010.sam" ftype="sam" />
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374 <conditional name="output_fmt_cond">
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375 <param name="output_fmt_select" value="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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376 <param name="output_quality" value="-O" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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377 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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378 <param name="outputs" value="r1,r2,s,other" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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379 <conditional name="idxout_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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380 <param name="idxout_select" value="yes"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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381 <param name="write1st" value="yes"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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382 <param name="barcode_tag" value="BC"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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383 <param name="index_format" value="n2i2"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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384 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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385 <output name="forward" file="10.1.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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386 <output name="reverse" file="10.2.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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387 <output name="singletons" file="10.s.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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388 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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389 <output name="i1" file="bc10.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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390 </test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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391 <!--# test -O flag with OQ tags-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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392 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/10.1.fq.expected', '2.fq' => 'bam2fq/10.2.fq.expected', 's.fq' => 'bam2fq/10.s.fq.expected', 'bc.fq' => 'bam2fq/bc10.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.010.sam");-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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393 <test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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394 <param name="input" value="bam2fq.010.sam" ftype="sam" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
395 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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parents: 0
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396 <param name="output_fmt_select" value="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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397 <param name="output_quality" value="-O" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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398 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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399 <param name="outputs" value="r1,r2,s,other" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
400 <conditional name="idxout_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
401 <param name="idxout_select" value="yes"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
402 <param name="write1st" value="yes"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
403 <param name="barcode_tag" value="BC"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
404 <param name="index_format" value="n2i2"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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405 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
406 <output name="forward" file="10.1.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
407 <output name="reverse" file="10.2.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
408 <output name="singletons" file="10.s.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
409 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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410 <output name="i1" file="bc10.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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411 </test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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412 <!--# tag output test with separators and -N flag-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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413 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/5.1.fq.expected', '2.fq' => 'bam2fq/5.2.fq.expected', 's.fq' => 'bam2fq/5.s.fq.expected', 'bc_split.fq' => 'bam2fq/bc_split.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -N \-\-index-format 'n*i*' \-\-i1 $$opts{path}/bc_split.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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414 <test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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415 <param name="input" value="bam2fq.005.sam" ftype="sam" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
416 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
417 <param name="output_fmt_select" value="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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418 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
419 <param name="outputs" value="r1,r2,s,other" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
420 <param name="read_numbering" value="-N"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
421 <conditional name="idxout_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
422 <param name="idxout_select" value="yes"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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423 <param name="write1st" value="yes"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
424 <param name="barcode_tag" value="BC"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
425 <param name="index_format" value="n*i*"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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426 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
427 <output name="forward" file="5.1.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
428 <output name="reverse" file="5.2.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
429 <output name="singletons" file="5.s.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
430 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
431 <output name="i1" file="bc_split.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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432 </test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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433 <!--# -t flag-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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434 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/6.1.fq.expected', '2.fq' => 'bam2fq/6.2.fq.expected', 's.fq' => 'bam2fq/6.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
435 <test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
436 <param name="input" value="bam2fq.005.sam" ftype="sam" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
437 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
438 <param name="output_fmt_select" value="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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439 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
440 <param name="outputs" value="r1,r2,s,other" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
441 <param name="copy_tags" value="-t" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
442 <param name="read_numbering" value="-N"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
443 <output name="forward" file="6.1.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
444 <output name="reverse" file="6.2.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
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diff changeset
445 <output name="singletons" file="6.s.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
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diff changeset
446 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
447 </test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
448 <!--# -T flag-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
449 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
450 <test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
451 <param name="input" value="bam2fq.005.sam" ftype="sam" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
452 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
453 <param name="output_fmt_select" value="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
454 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
455 <param name="outputs" value="r1,r2,s,other" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
456 <param name="copy_tags" value="-t" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
457 <param name="copy_arb_tags" value="MD,ia" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
458 <param name="read_numbering" value="-N"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
459 <output name="forward" file="7.1.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
460 <output name="reverse" file="7.2.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
461 <output name="singletons" file="7.s.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
462 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
463 </test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
464 <!--# -i flag with no index-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
465 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -i -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
466 <test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
467 <param name="input" value="bam2fq.005.sam" ftype="sam" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
468 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
469 <param name="output_fmt_select" value="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
470 <param name="ilumina_casava" value="-i" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
471 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
472 <param name="outputs" value="r1,r2,s,other" />
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
473 <conditional name="idxout_cond">
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
474 <param name="idxout_select" value="yes"/>
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
475 <param name="index_format" value="n2i2"/>
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
476 </conditional>
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
477 <param name="copy_tags" value="-t" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
478 <param name="copy_arb_tags" value="MD,ia" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
479 <param name="read_numbering" value="-N"/>
2
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
480 <output name="forward" file="11.1.fq.expected" ftype="fastqsanger" />
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
481 <output name="reverse" file="11.2.fq.expected" ftype="fastqsanger" />
720217c23995 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
482 <output name="singletons" file="11.s.fq.expected" ftype="fastqsanger" />
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
483 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
484 </test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
485 <!--# -i flag with index-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
486 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/8.1.fq.expected', '2.fq' => 'bam2fq/8.2.fq.expected', 's.fq' => 'bam2fq/8.s.fq.expected', 'i.fq' => 'bam2fq/8.i.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -i \-\-index-format 'n2i2' \-\-i1 $$opts{path}/i.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
487 <test>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
488 <param name="input" value="bam2fq.004.sam" ftype="sam" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
489 <conditional name="output_fmt_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
490 <param name="output_fmt_select" value="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
491 <param name="ilumina_casava" value="-i" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
492 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
493 <param name="outputs" value="r1,r2,s,other" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
494 <conditional name="idxout_cond">
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
495 <param name="idxout_select" value="yes"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
496 <param name="write1st" value="yes"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
497 <param name="barcode_tag" value="BC"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
498 <param name="index_format" value="n2i2"/>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
499 </conditional>
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
500 <output name="forward" file="8.1.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
501 <output name="reverse" file="8.2.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
502 <output name="singletons" file="8.s.fq.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
503 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
504 <output name="i1" file="8.i.fq.expected" ftype="fastqsanger" />
0
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
parents:
diff changeset
505 </test>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
parents:
diff changeset
506 </tests>
1
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
507 <help><![CDATA[
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
508 This tool uses `Samtools <http://www.htslib.org/>`_ to extract sequences from a
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
509 SAM or BAM file in FASTA or FASTQ format.
a8d69aee190e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
510 ]]>
0
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
parents:
diff changeset
511 </help>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
parents:
diff changeset
512 <expand macro="citations" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
parents:
diff changeset
513 </tool>