Mercurial > repos > devteam > samtools_flagstat
annotate samtools_flagstat.xml @ 7:5d3100bf5357 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
author | iuc |
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date | Thu, 27 Sep 2018 08:57:38 -0400 |
parents | 28eb6a47be96 |
children | 5fd05c7b42f8 |
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7
5d3100bf5357
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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1 <tool id="samtools_flagstat" name="Samtools flagstat" version="2.0.2"> |
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28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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2 <description>tabulate descriptive stats for BAM datset</description> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
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3 |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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4 <macros> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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5 <import>macros.xml</import> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
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6 </macros> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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7 <expand macro="requirements"/> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
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changeset
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8 <expand macro="stdio"/> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
diff
changeset
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9 <expand macro="version_command"/> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
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changeset
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10 |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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11 <command><![CDATA[ |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
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12 samtools flagstat '$input1' > '$output1' |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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13 ]]></command> |
0 | 14 |
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28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
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15 <inputs> |
7
5d3100bf5357
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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16 <param name="input1" type="data" format="sam,bam,cram" label="BAM File to report statistics of" /> |
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28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
diff
changeset
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17 </inputs> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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18 |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
diff
changeset
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19 <outputs> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
diff
changeset
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20 <data name="output1" format="txt" /> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
diff
changeset
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21 </outputs> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
diff
changeset
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22 |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
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23 <tests> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
diff
changeset
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24 <test> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
diff
changeset
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25 <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" /> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
diff
changeset
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26 <output name="output1" file="samtools_flagstat_out1.txt" /> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
diff
changeset
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27 </test> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
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diff
changeset
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28 </tests> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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29 <help><![CDATA[ |
0 | 30 **What it does** |
31 | |
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10b658bef71a
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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diff
changeset
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32 Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information:: |
0 | 33 |
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28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
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34 200 + 0 in total (QC-passed reads + QC-failed reads) |
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10b658bef71a
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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35 0 + 0 secondary |
10b658bef71a
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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36 0 + 0 supplementary |
10b658bef71a
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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37 0 + 0 duplicates |
10b658bef71a
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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38 25 + 0 mapped (12.50%:nan%) |
10b658bef71a
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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39 200 + 0 paired in sequencing |
10b658bef71a
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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40 100 + 0 read1 |
10b658bef71a
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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41 100 + 0 read2 |
10b658bef71a
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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42 0 + 0 properly paired (0.00%:nan%) |
10b658bef71a
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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43 0 + 0 with itself and mate mapped |
10b658bef71a
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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44 25 + 0 singletons (12.50%:nan%) |
10b658bef71a
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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45 0 + 0 with mate mapped to a different chr |
10b658bef71a
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
3
diff
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46 0 + 0 with mate mapped to a different chr (mapQ>=5) |
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28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
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47 ]]></help> |
28eb6a47be96
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
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48 <expand macro="citations"/> |
3 | 49 </tool> |